Immuno-amplification

ABSTRACT

A high-sensitivity, low-background immuno-amplification assay is provided, which offers a streamlined workflow suitable for high-throughput assays of clinically relevant samples, such as blood and other bodily fluids. The assay comprises the use of two proximity members that each comprise an analyte-specific binding component conjugated to an oligonucleotide. Binding an analyte brings the oligonucleotide moieties of the proximity members in sufficiently close contact that the oligonucleotides form an amplicon. The presence of the analyte then is detected through amplification of the amplicon and detection of the amplified nucleic acids. The sensitivity of the assay of the present invention is improved by preventing spurious or non-specific amplicon formation by proximity members that are not complexed with an analyte.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.10/826,654, filed on Apr. 19, 2004, which claims the benefit of thefiling date of U.S. Provisional Patent Application No. 60/463,712, filedApr. 18, 2003, the disclosures of which are incorporated herein byreference.

FIELD OF THE INVENTION

The invention relates to the novel application of analyte-specificbinding components and nucleic acid amplification to provide anultra-sensitive, high-throughput assay to detect and quantify an analytein solution.

BACKGROUND OF THE INVENTION

A primary goal in the areas of detection and quantification of analytesof interest is to develop a highly specific and sensitive assay system,capable of detecting minute quantities of an analyte in a complexmilieu, such as blood, serum, plasma, urine or other bodily fluids.Because diagnostically significant molecules may constitute or bepresent in extremely minute amounts relative to the other components ina bodily fluid, an acceptable assay format must discriminate analytesthat may represent a fraction of a percent of total biomaterial within asample. Conventional procedures use analyte-specific antibodies toprovide the requisite discrimination, but antibodies are limited bytheir cross-reactivity with other non-targeted analytes. Even forantibodies with high specificities, a small degree of cross-reactivitycould pose insurmountable problems if the analyte is present at minutequantities in a milieu rich in an analyte that binds the antibody with alow affinity.

Immuno-amplification has been used as a means of increasing thesensitivity of immunoassays. In this procedure, an antigen is contactedwith an antibody that is conjugated to a DNA marker molecule, which canbe amplified. Instead of detecting the presence of the antibody byconventional procedures, such as labeling the antibody-antigen complexwith a detectably labeled anti-antibody, the antigen-antibody-markerconjugate is detected indirectly through the amplification of the DNAmarker by a polymerase chain reaction (“PCR”). The amplified DNA thenmay be detected through conventional methods, such as the use of dyesthat fluoresce when they intercalate into double-stranded DNA. Thismethod, known as “immuno-PCR,” has been used to increase the theoreticalsensitivity of immunoassays by over 10,000-fold relative to conventionalassays that use anti-antibodies for detection; however, in practice thesensitivity of immuno-PCR is limited by non-specific binding of theantibody-nucleic acid conjugate to other analytes or to the surfaces ofthe supports used to house the reaction. Further, samples may becomecontaminated by residual amplified labels (“amplicons”) left over fromprevious reactions. This is problematic for applying this technique toclinically acceptable, high-throughput assays.

Several efforts have been made to alleviate these problems. Forinstance, investigators have used an immobilized antibody to capture theantibody-nucleic acid-antigen complex to a solid support, whichfacilitates the removal of non-complexed antigens and unboundantibody-nucleic acid conjugates prior to DNA amplification. In anothercase, two antibodies that are specific for different determinants of anantigen can be brought into proximity by binding the antigen. Eachantibody is modified with a single-stranded oligonucleotide moiety thatmay hybridize with an oligonucleotide of an adjacentantibody-oligonucleotide conjugate to form a double-stranded region. Thehybridization of the oligonucleotide moieties is facilitated by theproximity of the two antibodies when they are bound to the same antigen.The double-stranded region of DNA is then targeted for amplification toproduce a detectable signal that indicates the presence of the antigen.This technique advantageously improves the sensitivity of detectionbecause non-specific binding of either antibody alone is insufficient toallow the formation of the amplicon; however, the sensitivity of thismethod may be limited by, among other things, the non-specificinteraction of the antibody moieties with each other, which leads tospurious, antigen-independent amplicon formation.

Accordingly, there is a continuing need in the art to provide even moresensitive methods of analyte detection and quantification. Methods thatare useful in a clinical environment preferably are extremely selectivefor the desired analyte and easily adapted to high-throughout screeningmethodologies.

SUMMARY OF THE INVENTION

The present invention meets these needs by providing a high sensitivity,low background assay that offers a streamlined workflow suitable forhigh-throughput assays. The assay of the present invention detects andquantifies analytes by forming an analyte-specific amplicon through theinteraction of two “analyte-specific binding entities,” such asantibodies (a “proximity pair”), to different epitopes of the sameanalyte or to epitopes in analytes in close proximity. Each member ofthe proximity pair (a “proximity member”) comprises an analyte-specificbinding entity that is conjugated to a single-stranded nucleic acid,preferably DNA (an “oligonucleotide moiety” or “probe”). Theoligonucleotide moieties form an amplicon, directly or indirectly, whenthe proximity members are brought into close contact through theinteraction with a target or analyte(s) (“target” and “analyte” are usedinterchangeably throughout). Interaction of the proximity members withthe analyte brings the oligonucleotide moieties into close proximity,raising their effective local concentration relative to theconcentration of the oligonucleotide moieties of proximity members thatare not bound to an analyte. This concentration effect greatlyfacilitates the interaction of the two oligonucleotide moieties to forman amplicon relative to the oligonucleotide moieties of unboundproximity members. The proximity pair-analyte complex then is detectedby amplification of the amplicon, using DNA amplification technologiesthat are well-known in the art. Amplicon formation, therefore, is highlysensitive to the presence of the target because oligonucleotide moietiesthat have not interacted with other oligonucleotide moieties areincapable of being amplified, and the formation of the amplicon isgreatly facilitated by the increase in local concentration ofoligonucleotide moieties in the proximity pair-analyte complex.

The sensitivity of the assay of the present invention is advantageouslyimproved by preventing spurious and unwanted amplicon formation betweenproximity members in solution that are not complexed with an analyte.The present invention accomplishes this goal in part by providing one ormore hybridization blocker oligonucleotides (or “hybridizationblockers”), which hybridize to one or both of the oligonucleotidemoieties of the proximity members. The hybridization blockeradvantageously prohibits amplicon formation in solution betweenproximity members that are not complexed with an analyte. A method ofusing hybridization blockers comprises contacting an analyte with afirst and second proximity member in a reaction mixture, where theoligonucleotide moiety of at least one of the proximity membershybridizes to the hybridization blocker. The mixture is warmed or theionic strength is reduced sufficiently to cause the hybridizationblocker to dissociate, and the mixture is then cooled or the ionicstrength of the mixture is increased, allowing amplicons to form betweenanalyte-bound proximity members. In one embodiment, a majority of theanalyte-bound proximity members remain bound to the analyte during thewarming step. In another embodiment, the hybridization blocker is addedin molar excess over the oligonucleotide moieties of the proximitymembers. In yet another embodiment, the hybridization blocker hybridizesto a “splint oligonucleotide,” making the splint oligonucleotide unableto hybridize to an oligonucleotide moiety of a proximity member. In afurther embodiment, the hybridization blocker is removed from theoligonucleotide moiety of a proximity member by hybridizing with acomplementary sequence, also referred to as a “deblockeroligonucleotide” (or a “deblocker”). That is, the deblocker, when addedin excess, sequesters the hybridization blocker in a duplex so that thehybridization blocker is not as capable of hybridizing to theoligonucleotide moiety or to a splint oligonucleotide. The deblocker,therefore, reduces the presence of a hybrid between the hybridizationblocker oligonucleotide and its complementary sequences.

The hybridization blocker may comprise a hairpin loop at one of itstermini, where the hairpin structure serves as a double-stranded“primer” for DNA polymerase. For the purposes of the present invention,a “primer” is defined as a short stretch of nucleotides, typically ofDNA, that can hybridize to one strand of a template nucleic acid. Thedouble-stranded hybrid between the primer and its complementary sequenceprovides an initiation site for the extension of the primer by a DNApolymerase or reverse transcriptase, or for synthesis of RNA moleculesby RNA polymerase. The hybridization blocker may hybridize to theoligonucleotide moiety at a region downstream of the hairpin structure,so that extension by DNA polymerase removes the hybridization blockerfrom the oligonucleotide moiety by strand displacement. This embodimentadvantageously allows the hybridization blocker to be removed from theoligonucleotide moiety or splint oligonucleotide without the necessityof warming the reaction mixture, thereby avoiding or reducingdissociation of the proximity member with the analyte. In anotherembodiment, the hybridization blocker is added after the formation of aproximity pair-analyte complex and after the oligonucleotide moieties ofthe proximity pair have hybridized with each other. The hybridizationblocker hybridizes to the oligonucleotide moiety of at least one of theproximity members still in solution, thereby preventinganalyte-independent formation of amplicons by proximity pairs not boundto an analyte. In this embodiment as well, heating of the reactionmixture to reduce background signal is not required. Hairpin structuresmay also be used elsewhere. For example, one or both of theoligonucleotide moieties of the proximity members may comprise a hairpinstructure that blocks the formation of the amplicon. Hybridization ofoligonucleotide moieties through unpaired bases in the loop of thehairpin or adjacent to the hairpin (or, alternatively, gentle heating)disrupts the hairpin structure, thereby allowing amplicon formation andamplification.

The background signal may be advantageously further reduced by providinga solid phase capture oligonucleotide that either prevents ampliconformation until a specific release-oligonucleotide is provided orcaptures the proximity pair/analyte complex to allow removal of unboundcomponents.

Further advantages are provided by using universal reagents that can beharnessed to detect any analyte that can be bound by antibodies. Forexample, oligonucleotide moieties can be coupled to anti-Fc antibodiesor proteins A or G, which react with the immunoglobulin constant regionsof the antibody-analyte complex. In some embodiments, one or bothantibodies are replaced with any suitable specific analyte-targetingentity, such as an aptamer, a ligand specific for a receptor analyte, ora receptor that is specific for a ligand analyte. This replacement ofone or both antibody moieties reduces spurious amplicon formation thatwould otherwise result from non-specific interactions between theantibody moieties. Among other suitable specific analyte-targetingentities are functional fragments of antibodies, such as Fc, Fv, Fab′ orF(ab′)₂ fragments. The reduction in the size of the antibody structurenot involved in antigen binding is believed to reduce the non-specificinteractions of antibodies with each other without reducing the specificinteraction with antigens or analytes.

The advantages provided by the present invention allow a high-throughoutand extremely sensitive assay that can be used to detect and quantifyanalytes in clinically relevant samples, such as blood and other bodilyfluids. Analytes that may be detected and quantified by the methods ofthe present invention may occur in unprecedented minute quantities in acomplex mixture (e.g., a bodily fluid). In one embodiment, the presentinvention is used to detect about 80 fg/ml of an analyte such as acytokine. This translates to an ability to detect a molar concentrationof at least about 10 fM of such small molecular weight analytes.

The present invention accordingly provides various methods to detectand/or quantify target analytes, as well as compositions that are usefulin carrying out the methods of the present invention. For example, anysuitable method of amplification may be used in the methods of theinvention. Such methods include, but are not limited to, PCR (describedin U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188),Strand Displacement Amplification (“SDA”; see Walker et al., Proc. Nat'lAcad. Sci. USA 89: 392 (1992); Walker et al., Nucl. Acids Res. 20: 1691(1992); and U.S. Pat. No. 5,270,184, the disclosure of which is herebyincorporated in its entirety by reference), thermophilic StrandDisplacement Amplification (“tSDA”; see U.S. Pat. Nos. 5,648,211 and5,744,311, the disclosures of which are hereby incorporated in theirentirety by reference), Self-Sustained Sequence Replication (“3SR”; seeGuatelli et al., Proc. Nat'l Acad. Sci. USA 87: 1874-78 (1990)), NucleicAcid Sequence-Based Amplification (“NASBA”; see U.S. Pat. No.5,130,238), Qβ replicase system (see Lizardi et al., BioTechnology6:1197 (1988)); Ligase Chain Reaction (“LCR”; see U.S. Pat. No.5,427,930); transcription-mediated amplification (“TMA”; Hirose et al.,Clin. Chem. 44:2446-2452 (1998)); and transcription-based amplification(see Kwoh et al., Proc. Nat'l Acad. Sci. USA 86: 1173-77 (1989)). Apreferred method of amplification is SDA.

The amplicon itself may be formed by a number of methods, including thehybridization of adjoining oligonucleotide moieties of the proximitypair. For example, adjoining oligonucleotide moieties may hybridize overall or a segment of their length. If adjoining oligonucleotideshybridize at a portion of the respective termini, then the resultingduplex may be extended, using a DNA polymerase. When the amplificationreaction comprises a SDA reaction, restriction endonuclease recognitionsites may be incorporated on one or both of the oligonucleotide moietiesof the proximity members or their extension products.

The amplicon also may be formed by contacting the oligonucleotidemoieties of the proximity pair with an oligonucleotide “splint” thathybridizes to the respective termini of the oligonucleotide moieties.The oligonucleotide splint may further comprise a restrictionendonuclease recognition site and a first sequence that is complementaryto a first oligonucleotide probe. The oligonucleotide moiety of a firstproximity member additionally may comprise a second sequence that iscomplementary to a second oligonucleotide probe. The splint may be usedin a method that comprises adding the first and second probes andextending the sequence complementary to the oligonucleotide moietieswith a DNA polymerase. The oligonucleotide moiety of the secondproximity member is displaced, leaving the amplicon attached to thefirst proximity member through the conjugation with the oligonucleotidemoiety of the first proximity member. For the purpose of the presentinvention, a displaced oligonucleotide moiety that is not amplified isreferred to as a “tether oligonucleotide.” “Displacing,” for the purposeof the present invention, may be accomplished by such methods as stranddisplacement or hydrolysis of the displaced strand catalyzed by apolymerase having a 3′-5′ exonuclease activity. The method furthercomprises amplifying the amplicon through any of the well-known methodsof amplification, such as SDA.

In another embodiment, the amplicon advantageously is released from thecomplex of the proximity pair and the analyte, which reduces thebackground by eliminating signal from antibody-oligonucleotideconjugates that are absorbed to the assay support surfaces. In thisembodiment, two oligonucleotide splints are used to form the amplicon,and both of the oligonucleotide moieties of the proximity members aretether oligonucleotides. A first bridging probe hybridizes to the 5′ endof the oligonucleotide moiety of a first proximity member, and a secondbridging probe hybridizes to the 5′ end of the oligonucleotide moiety ofa second proximity member. The first and second bridging probeshybridize with each other at their respective 3′ ends. Upon extensionwith a polymerase, the oligonucleotide moieties of the first and secondproximity members are displaced, and the amplicon is released from theremaining components of the proximity pair-analyte complex. The ampliconis then amplified by any of the well-known methods of amplification.

In an alternative embodiment, the proximity pair-analyte complex isimmobilized on a solid support. The amplicon is released from thecomplex into solution, using the method set forth above, while theremaining components of the proximity pair-analyte remain bound to thesolid support. In this embodiment, the solution containing the ampliconcan be removed entirely from the remaining components of the complexprior to amplification, which reduces background even further.

The use of two splint oligonucleotides in the manner set forth aboveallows a method of target-mediated probe cycling. This method comprisescontacting a proximity pair with first and second splintoligonucleotides, extending the complement of the oligonucleotidemoieties with DNA polymerase, thereby displacing the amplicon from theproximity pair, amplifying the amplicon, and contacting the proximitypair with additional first and second splint oligonucleotides. Thesplint oligonucleotides optionally may hybridize to the 3′ end of theoligonucleotide moiety of a first proximity member and the 5′ end of theoligonucleotide moiety of a second proximity member. The splintoligonucleotides optionally may hybridize to the 3′ end of theoligonucleotide moiety of a first proximity member and the 3′ end of theoligonucleotide moiety of a second proximity member. Both of the splintoligonucleotides optionally may hybridize to complementary sequences ofa third splint oligonucleotide that forms a bridge between the first andsecond splint oligonucleotides.

In a further embodiment, an oligonucleotide splint may comprise asequence encoding a RNA polymerase promoter in a region of the probethat does not hybridize with an oligonucleotide moiety and that isupstream, i.e., located in a 5′ orientation, of a first sequence that iscomplementary to a first oligonucleotide probe. The oligonucleotidemoiety of a first proximity member additionally may comprise a secondsequence that is complementary to a second oligonucleotide probe. Thesplint may be used in a method that comprises adding the first andsecond probes and extending the sequence complementary to theoligonucleotide moieties with a DNA polymerase. The oligonucleotidemoiety of the second proximity member is displaced by the extendedstrand, leaving the amplicon attached to the first proximity member,where the amplicon comprises a now intact, double-stranded RNApolymerase binding site. The method further comprises transcribingsingle-stranded RNAs by contacting the RNA polymerase binding site withan RNA polymerase. The RNAs may be detected by means well-known in theart, including hybridization with labeled probes. In addition to stranddisplacement, the oligonucleotide moiety of the second proximity memberalso may be removed by using a DNA polymerase with 5′-3′ exonucleaseactivity, such as Tag DNA polymerase.

Alternatively, the single-stranded RNA transcript is contacted with aprimer that hybridizes to the RNA at its 3′ region, allowingtranscription of the RNA by reverse transcriptase to generate a DNA-RNAhybrid. Digesting this DNA-RNA hybrid with RNase H yields acomplementary DNA strand. Contacting this DNA strand with a primer,which comprises the complement to the RNA polymerase binding site,regenerates the intact double-stranded RNA polymerase binding site. TheDNA strand is contacted with an RNA polymerase, which catalyzes thesynthesis of a single-stranded RNA transcript. The steps of contactingthe transcript with a primer, contacting the primer-transcript hybridwith a reverse transcriptase, digesting the DNA-RNA hybrid, andcontacting the resulting single-stranded DNA with a primer thatreconstitutes the RNA polymerase binding site may be repeated, resultingin exponential amplification of the amplicon.

The amplification method of the present invention may be conductedentirely in solution in a “homogeneous format,” or it may comprise theimmobilization of components of the reaction to a solid support in a“heterogeneous format.” For a method of amplification using theheterogeneous format, a proximity member, an analyte or a complexbetween a proximity member or pair and an analyte is immobilized to asolid support, such as a particle or the surface of a reaction vessel.For this purpose, a proximity member or analyte comprises anoligonucleotide moiety complementary to an oligonucleotide conjugated tothe support (a “capture oligonucleotide”). The hybrid formed between theoligonucleotide moiety of the proximity member or analyte and thecapture oligonucleotide may comprise a restriction endonucleaserecognition site. The captured proximity member or analyte is releasedfrom the solid support by a method comprising contacting the recognitionsite with the appropriate restriction endonuclease. Alternatively, themethod to release the bound proximity member or analyte comprisesdenaturing the hybrid between the capture oligonucleotide and theoligonucleotide moiety of the proximity member or analyte by such meansas increasing the temperature, decreasing ionic strength, changing thepH of the reaction mixture, or adding chelating agents that promotehybrid denaturation. In yet another embodiment, the captureoligonucleotide comprises a scissile linkage that is particularlysusceptible to cleavage by, for example, physical, enzymatic, chemicalor photochemical means. In a further embodiment, the captureoligonucleotide or the oligonucleotide moiety of the proximity member oranalyte comprises a complementary sequence to a primer. The primer iscapable of hybridizing to the hybrid formed between the captureoligonucleotide and the oligonucleotide moiety of the proximity memberor analyte. The oligonucleotide moiety of the proximity member oranalyte then may be displaced from the hybrid by polymerase chainextension and strand displacement. In a related embodiment, the captureoligonucleotide is capable of forming a hairpin structure that forms atemplate for polymerase extension, causing release of a capturedproximity member or analyte by strand displacement.

The hybrid between the capture oligonucleotide and the oligonucleotidemoiety of the proximity member or analyte optionally may comprise an RNAsequence. The proximity member or analyte is released from the surfaceby contacting the hybrid with an RNase, such as RNase H. In oneembodiment, the oligonucleotide moiety of a proximity member thathybridizes to the capture oligonucleotide is the oligonucleotide moietythat is involved in forming the amplicon. The oligonucleotide moietycannot form an amplicon as long as it remains hybridized to the captureoligonucleotide, but release of the oligonucleotide moiety from thehybrid by strand displacement, for example, allows the amplicon to form.

Amplification using the heterogeneous format may comprise contacting ananalyte with a first proximity member in a reaction mixture, adding asecond proximity member that is immobilized to a solid support or iscapable of being immobilized to a solid support under conditionssufficient to form a proximity pair-analyte complex that comprises anamplicon, washing the bound proximity pair-analyte complex to removeproximity members that are not immobilized to the solid support,amplifying the amplicon, and detecting the amplification product. Thesecond proximity member may be added before, after or simultaneouslywith the first proximity member. Optionally, the second proximity membermay be immobilized to the solid support by a scissile linkage, which iscleaved after washing but prior to amplification. The method ofimmobilizing the proximity member to a solid support and cleaving theproximity member from the solid support that are set forth above may beused. Further, any of the methods for forming the amplicon set forthabove, such as the method that comprises adding a splintoligonucleotide, may be used in the heterogeneous format.

The present invention advantageously provides universal components thatcan be used in any of the amplification methods set forth above. In apreferred embodiment, an analyte is contacted with a first antibody thatbinds a first epitope and a second antibody that binds a second epitope,where the first and second epitopes and antibodies may be the same ordifferent. Optionally, the first and second antibodies may each belabeled with a different hapten moiety (e.g., biotin, fluorescein,digoxigenin, trinitrophenol, dinitrophenol and the like). The antibodiesare contacted with a universal component that comprises one or moreproximity members that specifically bind the first and/or secondantibodies to form a proximity pair comprising an amplicon. Theuniversal component may be, for example, protein A or protein G,conjugated to a oligonucleotide moiety. Alternatively, the universalcomponent may be an anti-immunoglobulin constant region antibody that isconjugated to an oligonucleotide. If the first and second antibodies arelabeled with hapten moieties, then the universal component may beantibodies (or other agents such as streptavidin) that are specific forthe particular hapten label. The use of universal componentsadvantageously eliminates the necessity of modifying eachanalyte-specific analyte-binding entity with an oligonucleotide moiety.

The proximity members may be antigens that are conjugated to twodifferent oligonucleotide moieties. The analyte in this embodiment is anantigen-specific antibody, which may be an IgG or any other type ofantibody. The binding of the antigen-oligonucleotide conjugates by theantibody forms a proximity pair that may comprise an amplicon, when thebound antigen-oligonucleotide conjugates comprise differentoligonucleotide moieties. This method, therefore, can be used to detectthe presence of particular antibodies with great sensitivity.

The invention also provides a kit, which may comprise individual orcombined components and reagents that are useful for carrying out themethod of the present invention, such as buffers, chemical reagents,enzymes, oligonucleotides, proximity members, and instructions for theuse of these components or reagents. For example, the kit may compriseoligonucleotide amplification primers that are suitable for carrying outthe amplification and detection methods described herein. The kit mayadditionally comprise reagents and solutions for detecting amplifiednucleic acids, such as radiolabels, enzyme substrates, antibodies, andthe like. Suitable solutions and reagents are well-known and aredescribed in Sambrook et al., Molecular Cloning, A Laboratory Manual(3rd ed., 2001), for example. The components of the kit are packagedtogether in a common container, typically including instructions forperforming embodiments of the methods disclosed herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows mixing of antigens and oligonucleotide-conjugatedantibodies.

FIG. 1B shows hybridization of adjacent probes.

FIG. 1C shows a polymerase extension and restriction enzyme nicking.

FIG. 1D shows extension, displacement and linear amplification.

FIG. 1E shows hybridization, polymerase extension, nicking andexponential amplification.

FIG. 1F shows mixing of antigens and oligonucleotide-conjugatedantibodies.

FIG. 1G shows hybridization of adjacent probes.

FIG. 1H shows extension of probes with a polymerase.

FIG. 1I shows denaturation of a probe-extension duplex and the bindingof SDA primers.

FIG. 1J shows amplicon formation from hybridized probes of oppositesequence orientation.

FIG. 2A shows hybridization of a splint oligonucleotide.

FIG. 2B shows ligation of adjacent probes.

FIG. 2C shows DNA polymerase extension and displacement.

FIG. 2D shows the use of two hybridized proximity probes to ligate athird probe.

FIG. 2E shows the use of two hybridized proximity probes in oppositesequence orientation to ligate a third probe.

FIG. 3A shows a single-tether probe.

FIG. 3B shows extension and displacement of a single-tether probe.

FIGS. 3C and D show nicking, extension, displacement and capture.

FIG. 3E shows splint oligonucleotides having a 3′/3′ configuration.

FIG. 3F shows extension/displacement of splint oligonucleotides.

FIG. 3G shows target-mediated probe cycling.

FIG. 3H shows splint oligonucleotides having a 5′/3′ configuration.

FIG. 3I shows splint oligonucleotides having a 5′/5′ configuration.

FIG. 3J shows splint oligonucleotides having a 3′/3′ configuration.

FIG. 3K shows splint oligonucleotides having a 3′/3′ configuration.

FIG. 3L shows displacement of splint oligonucleotides from a capturedcomplex.

FIG. 4A shows a simple competitive hybridization blocker.

FIG. 4B shows a recessed competitive hybridization blocker.

FIG. 4C shows a disabling hybridization blocker.

FIG. 4D shows a displaceable hybridization blocker.

FIG. 4E shows a self-displacing hybridization blocker.

FIG. 4EE shows the use of a 3′ probe tail to stabilize a probe-blockerduplex.

FIG. 4F shows competitive hybridization blocker in a binary immuno-SDAreaction.

FIG. 4G shows a disabling hybridization blocker in a binary immuno-SDAreaction.

FIG. 4H shows step-wise blocking in a binary immuno-SDA reaction.

FIG. 4I shows the post-binding addition of hybridization blockers in abinary immuno-SDA reaction.

FIG. 5A shows a splint oligonucleotide hybridization.

FIG. 5B shows extension and displacement.

FIG. 5C shows RNA polymerase activity, hybridization and extension.

FIG. 5D shows RNase H activity, hybridization and extension.

FIG. 6A-C show restriction endonuclease-mediated release of an attachedconjugate.

FIGS. 6D and E show polymerase- and restriction endonuclease-mediatedrelease.

FIG. 6F shows physical release.

FIGS. 6G and 6GG show scissile linkages and chemical cleavage.

FIG. 6H shows oligonucleotide displacement.

FIGS. 6I and J show oligonucleotide extension.

FIGS. 6K and L show RNase H release.

FIG. 6M shows a self-priming capture/displacement oligonucleotide.

FIG. 6N shows the involvement of the displaced probe moiety in theformation of an amplicon.

FIG. 7A shows immobilization of a first proximity member byhybridization of an oligonucleotide moiety of the first proximity memberwith a capture oligonucleotide.

FIG. 7B shows the binding of a target analyte to the immobilized firstproximity member.

FIG. 7C shows, the formation of an immobilized two-site “sandwich” bythe binding of a second proximity member to the immobilized complexbetween the target analyte and the first proximity member.

FIG. 7D shows a mechanism by which a target-independent amplicon mayform.

FIGS. 7E-H show the use of a hybridization blocker oligonucleotide tosuppress probe-probe interactions that lead to target-independentamplicon formation.

FIG. 7I shows the release of an immobilized complex between a targetanalyte and two proximity members using low ionic strength.

FIG. 7J shows the use of a capture oligonucleotide and release in aheterogeneous assay format.

FIG. 8A-C show heterogeneous immuno-amplification.

FIG. 8D shows heterogeneous immuno-amplification with a scissilelinkage.

FIG. 9 shows heterogeneous immuno-amplification with splintoligonucleotides.

FIG. 10 shows a universal immuno-amplification system.

FIG. 11A shows hairpin release probes.

FIG. 11B shows hairpin hybridization blocker probes.

FIG. 11C shows displacement of hairpin hybridization blocker probes.

FIG. 12 shows detection of antigen-specific immunoglobulin.

FIG. 13 presents a map of representative probes, primers, and tetheroligonucleotides for binary immuno-SDA (see SEQ ID NOS.:19, 6, 10, 11,9, 1 and 18, respectively, in order of appearance).

FIGS. 14A-E show the use of a 3′ capped oligonucleotide moiety to formamplicons attached to a first proximity member and to a second proximitymember, but not to both proximity members simultaneously.

FIG. 15A shows a two-color, real-time fluorescence profile forimmuno-SDA detection of IL-8.

FIG. 15B shows a calibration line for quantification of IL-8.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Minute quantities of an analyte may be detected with great sensitivityby the present invention. The invention provides conjugates ofanalyte-specific binding factors, such as antibodies, conjugated tooligonucleotide moieties that can form an amplicon. The conjugationbetween antibodies and other proteins with oligonucleotides is known inthe art and taught, for example, in U.S. Pat. No. 5,849,878 and No.5,665,539, which are incorporated by reference in their entirety herein.If the analyte-specific binding factor is a nucleic acid, for example,an aptamer, then the analyte-specific binding factor and theoligonucleotide or probe moiety may be synthesized in one contiguousstrand using chemical synthesis methods known in the art. The term“conjugate” still applies to such aptamer-probe entities. The conditionsfor establishing an amplicon by adjoining oligonucleotides that are eachconjugated to an antibody are also known and taught in U.S. Pat. No.6,511,809, for example. Conditions and methodologies for amplifyingamplicons and for detecting their presence are also known in the art, astaught in U.S. Pat. No. 6,511,809 and U.S. Patent ApplicationPublication No. 2002/00674779, both incorporated herein by reference intheir entirety. The use of labeled probes for the detection ofamplification products, for example, also is taught in U.S. Pat. No.5,928,869, No. 5,919,630; No. 5,935,791; No. 6,316,200; and No.6,379,888, all incorporated herein by reference in their entirety. U.S.Pat. No. 5,840,487 teaches the use of internal controls for isothermalnucleic acid amplification reactions and is also incorporated herein byreference in its entirety.

According to the present invention, a preferred method of amplificationby SDA is detailed in FIG. 1. Ab1 and Ab2 are antibodies that recognizeadjacent epitopes 1 and 2 and that are conjugated to oligonucleotideprobes P1 and P2, respectively (FIG. 1A). The antibodies arerepresentative, but not limiting examples, of the analyte-specificbinding components that are useful in the present invention. Forinstance, useful analyte-specific binding components known in the artinclude functional fragments of antibodies, such as Fc, Fv, Fab′ andF(ab′)₂ fragments. Other examples of analyte-specific binding componentsinclude aptamers, ligands specific for a receptor analyte, or a receptorthat is specific for a ligand analyte. Further, it will be understood bythe skilled artisan that various different types of analyte-specificbinding components may be used in combination. “Oligonucleotide probes”and “oligonucleotide moieties” are used synonymously for the purposes ofthe present invention. The term “oligonucleotide” should not beunderstood as placing an upper size limit on the nucleic acid moietiesfor the purpose of this invention; therefore, “oligonucleotide” issynonymous with “polynucleotide,” as used herein. For the purposes ofthe present invention, an oligonucleotide may be composed in whole or inpart by DNA, RNA or an analogue or derivative thereof. In thisembodiment, P1 and P2 comprise complementary 3′ terminal sequences andupstream SDA nick sites. The use of nick sites for SDA and theconditions for SDA in general are described in U.S. Pat. No. 5,919,630;No. 5,846,726; and No. 6,054,729, which are incorporated herein byreference in their entirety. The 3′ ends of P1 and P2 hybridize to oneanother when the two antibodies to which they are linked are held inclose proximity by binding to their respective epitopes (FIG. 1B).Conditions conducive to nucleic acid hybridization, including the numberof base pairs or mismatches in the hybridized portion of a nucleic acidand the temperature and ionic strength of the buffer in which thehybridization occurs, are well-known in the art and are generallydescribed, for example, in Sambrook et al., Molecular Cloning, ALaboratory Manual (3rd ed., 2001). The bulk solution concentration ofAb1 and Ab2 is relatively low compared with that at the surface of theantigen, such that antigen-independent hybridization of P1 and P2 isminimized. DNA polymerase is then used to fill in the recessed 3′ endsof the P1:P2 hybrid (FIG. 1C). This serves to generate double-strandedrestriction sites that are recognized by the SDA nicking enzyme. Anicking enzyme catalyzes the cleavage of only one strand of thedouble-stranded DNA template. Nicking and polymerase extension from thesite of the nick displaces the downstream DNA strand into solution andregenerates the nick site (FIG. 1D). Repeated cycling of the nicking andextension/displacement steps may be used to produce multiple copies ofthe displaced strand. The displaced strand is captured by acomplementary SDA primer (FIG. 1E). Extension from the 3′ ends of thecaptured strand and hybridized SDA primer produces a double-stranded DNAmolecule that may be exponentially amplified through a series ofintermediates. In an alternative embodiment, only one of theoligonucleotide probes P1 and P2 comprises an SDA nick site.

In another embodiment (FIG. 1F-I), probes P1 and P2 lack SDA nick sites,but comprise instead sequences c and d′, which also are present on SDAprimers SP2 and SP1, respectively (see FIG. 1I). Extension of the 3′ends of P1 and P2 creates a duplex containing complementary sequence don the extension product of P1 and complementary sequence c′ on theextension product of P2 (see FIG. 1H). The strands of the duplexedextension products are then separated by, for example, heating,whereupon SDA primers SP1 and SP2 hybridize to the complement of thenewly synthesized sequences d and c′ of the extended probes. Theextended probes optionally may comprise a sequence located 3′ to thebinding sites of the SDA primers, shown as sequence e of extended P1 andsequence b′ of extended P2. These sequences hybridize with bumperprimers SB1 and SB2 (see FIG. 1I). During SDA, the SDA primers SP1 andSP2 are extended by polymerase (not shown). Extension of the bumperprimers, if present, serves to displace the SDA primer extensionproducts from the probe strands, and the displaced strands are thenamplified by SDA, as described in U.S. Pat. No. 5,270,184; No.5,919,630; No. 5,846,726; and No. 6,054,729. In the event that theextended probes do not contain sequences 3′ to the SP1 and SP2 bindingsites (not shown), the 3′ ends of the probes that are hybridized to SDAprimers are extended by polymerase, creating nickable restriction sitesthat allow subsequent nicking and strand displacement by SDA asdescribed above.

In preceding embodiments, oligonucleotide moieties (P1 and P2) wereconjugated to their respective analyte binding entities (Ab1 and Ab2)through linkages located at or near their 5′ termini. In an alternativeembodiment illustrated in FIG. 1J, conjugate Ab1-P1 is formed through alinkage located at or near the 3′ terminus of P1, while conjugate Ab2-P2is formed through a linkage located at or near the 5′ terminus of P2. P1comprises sequence (a b c d e f) (read 5′ to 3′), and P2 comprisessequence (j′ i′ h′ g′ f′ e′) (read 5′ to 3′). Ab2-P2 further comprisesan extendible 3′ end (i.e., a 3′ terminal hydroxyl group). As shown,sequence (e f) of P1, which is capable of hybridizing to sequence (f′e′) of P2, is located 5′ of the site at which P1 is conjugated to Ab1,whereas (f′ e′) is located 3′ of the site at which P2 is conjugated toAb2. Probes P1 and P2 are, therefore, said to be linked to theirrespective analyte binding entities (Ab1 or Ab2) in opposite sequenceorientations. When P1 and P2 are brought into close proximity, forexample, through binding of their respective proximity members to thesame target analyte molecule, sequence (e f) of P1 hybridizes with (f′e′) of P2, as depicted on the left side of FIG. 1J. Polymerase may thenbe used to extend the 3′ end of P2 to create an extension product (i.e.,amplicon) P2-ext containing the new sequence, as shown. P2-ext may thenbe detected by methods known in the art, making use of all or part ofthe new sequence (d′ c′ b′ a′) to distinguish P2-ext from unconvertedP2. For example, P2-ext may be amplified by nucleic acid amplificationmethods described above. P2-ext may be separated from P1 by heating thesolution, and a primer may hybridize to the new sequence at the 3′ endof P2-ext and be extended to create a complement of P2-ext. Subsequentrounds of amplification may involve separation of the complement fromP2-ext and hybridizing to the complement a different primer comprised ofa sequence located near the 5′ end of P2. In a preferred embodiment,sequence b will contain the single-strand component of a recognitionsequence for an SDA-compatible restriction enzyme. Formation of P2-extthen creates a double-stranded recognition sequence that is nicked bythe restriction enzyme. Extension from the nick creates a new strandthat is complementary to P2-ext, regenerating the nickable recognitionsequence. This product may be amplified and detected by SDA methodsreferred to above. Optionally, sequence i′ of P2 may also comprise thesingle-strand component of a recognition sequence for SDA and, if so,the duplex formed between P2-ext and its full-length complementarystrand will contain two nickable restriction enzyme recognitionsequences. In another embodiment, sequence b may be a single-strandcomponent of an RNA polymerase promoter site. Formation of P2-ext thencreates a double-stranded RNA polymerase promoter, which may be used todirect the activity of an RNA polymerase to synthesize RNA moleculesthat are complementary to sequence (j′ i′ h′ g′ f′ e′ d′ c′) of P2-ext.These RNA molecules may be detected directly, or they may be furtheramplified by methods such as 3SR, NASBA, TMA, or transcription-basedamplification. Optionally, sequence i′ of P2 may comprise thesingle-strand component of an RNA polymerase promoter. In this case,extension of a primer hybridized to the 3′ end of P2-ext would create adouble-stranded promoter site that can be used to direct the activity ofthe RNA polymerase to synthesize RNA molecules comprising the sequence(h′ g′ f′ e′ d′ c′ b′ a′), which may be detected directly or amplifiedusing the aforementioned methods. Regardless of the method of detectionOr amplification of P2-ext, the embodiments depicted in FIG. 1J compriseprobe moieties P1 and P2 that are linked to their respectiveanalyte-binding elements Ab1 and Ab2 in opposite sequence orientations,and the two probes hybridize to each other in a target-mediated process,creating a duplex with an extendible 3′ end that is subsequentlyextended to create an amplicon. In the absence of target-analyte, P1 andP2 will not be brought into close proximity, and P2-ext will not formexcept through spurious (i.e., target-independent) interactionsmentioned below, which may be suppressed by hybridization blockingoligonucleotides, also described below. P2-ext is, therefore, producedas a consequence of the presence of target analyte and in proportion tothe quantity of target analyte present. Determination of the quantity ofP2-ext produced may, therefore, be used to determine the quantity oftarget analyte present in a sample.

FIGS. 2A-C detail a representative use of a splint oligonucleotide. Ab1and Ab2 are antibodies that recognize adjacent epitopes 1 and 2 and areconjugated to oligonucleotide probes P1 and P2, respectively (FIG. 2A).P1 is conjugated to Ab1 through a linkage located at or near its 5′terminus, and it comprises a 3′ terminal hydroxyl group and upstream SDAnick site. Probe P2 is conjugated to Ab1 at its 3′ end, and it comprisesan SDA primer binding site and 5′ terminal phosphate group. The sequenceof the splint oligonucleotide S is complementary to the 3′ end of probeP1 and the 5′ end of probe P2 such that, when held in close proximity bybinding of the antibodies to their respective epitopes, oligonucleotidesP1 and P2 form a double-stranded hybrid with the splint S. Whenhybridized to the splint oligonucleotide S, the 3′-OH of P1 and 5′-PO₄of P2 are adjacent, and DNA ligase is used to catalyze the formation ofa phosphodiester bond linking the P1 and P2 sequences (FIG. 2B). SDAprimer SP1 hybridizes to probe P2 upstream of splint oligonucleotide S.A strand-displacing DNA polymerase extends from the 3′ ends of primerSP1 and splint oligonucleotide S. Extension of primer SP1 displaces theextension product of splint oligonucleotide S (FIG. 2C) and creates adouble-stranded DNA molecule with SDA restriction enzyme nick sites ateither end. This molecule is analogous to that depicted in FIG. 1C.Nicking, polymerase extending from the nick, and displacing thedownstream strand leads to exponential amplification (FIGS. 1D-E). Inone embodiment, the probe P1 does not comprise a SDA nick site. Inanother embodiment, the splint oligonucleotide S comprises a 3′ cap toprevent 3′ extension of the splint S.

FIGS. 2D and 2E illustrate an alternative embodiment fortarget-mediated, ligase-catalyzed amplicon formation using a pair ofproximity members. Probes P1 and P2 are linked, or conjugated, to theirrespective antibodies (or other analyte binding entities) Ab1 and Ab2.Conjugation may occur through linkages at or near the 5′ termini of bothprobes, as shown in FIG. 2D, or one of the two probes (P1) may beconjugated through a linkage located at or near the 3′ end of the probe.P1 comprises sequence (a b c d e f) (read 5′ to 3′), and P2 comprisessequence (j′ i′ h′ g′ f′ e′) (read 5′ to 3′). Conjugate Ab2-P2 furthercomprises a 3′ terminal hydroxyl group. In configurations depicted byeither FIG. 2D or 2E, sequences (e f) of P1 and (f′ e′) of P2 arecapable of hybridizing to each other. A third probe P3 comprisessequence (d′ c′ b′ x′ y′) and further comprises a 5′ terminal phosphategroup. P3 is capable of hybridizing to sequence (b c d) of probe P1(adjacent to sequence (e f) of P1). In the presence of target analyte,P1 and P2 are brought into close proximity and form a duplex throughhybridization of sequences (e f) and (f′ e′). Probe P3 may be hybridizedto P1, as shown, either before or after P1 and P2 hybridize. In eithercase, the 5′ nucleotide of P3 is positioned adjacent to the 3′nucleotide of P2 and, in this configuration, P2 and P3 may be covalentlylinked together by DNA ligase (or other ligation mechanism) to form theamplicon P2:P3, as shown. P2:P3 may then be detected by various methods,including amplification, such as those described above for embodimentsdepicted in FIG. 1J. In this case, however, sequence x′ and/or y′ willbe used as sites for primer hybridization. In the absence of targetanalyte, P1 and P2 will not be brought into close proximity, and P2:P3will not form, except through spurious (i.e., target-independent)interactions between P1 and P2 mentioned below, which may be suppressedby hybridization blocking oligonucleotides also described below. P2:P3is, therefore, produced as a consequence of the presence of targetanalyte and in proportion to the quantity of target analyte present.Determination of the quantity of P2:P3 produced may, therefore, be usedto determine the quantity of target analyte present in a sample.Hybridization blockers are not required during amplification ofamplicons formed by ligating oligonucleotide moieties of proximitymembers because probes that can be joined by ligation typically do notform hybrids with each other and therefore do not have the potential toundergo spurious probe conversion during amplification involving 3′extension of oligonucleotides.

FIG. 3 shows a representative embodiment of the present invention thatcomprises a splint oligonucleotide designed to bridge the gap betweentwo oligonucleotide moieties of proximity members. In one embodiment(FIG. 3A), one of the proximity antibodies Ab1 is conjugated through alinkage at or near the 3′ end of a tether-oligonucleotide. Hereafter, a“tether oligonucleotide” denotes an oligonucleotide moiety that isdisplaced from the amplicon but remains conjugated to theanalyte-specific binding moiety. The tether oligonucleotide TO iscomplementary to a segment (preferably at or near the 5′ end) of thesplint oligonucleotide P1. Splint oligonucleotide P1 may furthercomprise a primer sequence to facilitate amplification of the convertedprobe and a detector region to facilitate detection of the convertedprobe. P1 may also comprise a restriction recognition sequence tofacilitate amplification by SDA. In addition, the 3′ sequence of thesplint oligonucleotide is complementary to the 3′ end of probe P2 thatis conjugated through its 5′ terminus to antibody Ab2. As depicted inFIG. 3A, the 5′ end of P1 is complementary to the tether oligonucleotideTO, which is attached to Ab1. Optionally, the tether oligonucleotide maybe complementary to a sequence not on the 5′ end of P1. When antibodiesAb1 and Ab2 are bound to their respective epitopes, splintoligonucleotide P1 is able to hybridize to both TO and P2 (FIG. 3A).Extension from the 3′ ends of probe P2 and the splint oligonucleotidedisplaces tether oligonucleotide TO and creates a double-stranded DNAmolecule linked to antibody Ab2 (FIG. 3B). Nicking of thisdouble-stranded product, extending with polymerase, and displacing thedownstream strand generates a single-stranded oligonucleotide that mayform a hybrid with a complementary SDA primer (FIG. 3C). This leads toexponential amplification through a succession of intermediate nicking,extending, displacing and priming events (FIG. 3D).

FIG. 3E depicts a second embodiment for bridging the gap betweenantibodies. In this configuration, each antibody (Ab1 and Ab2) isconjugated with a different tether oligonucleotide, a′ for Ab1 and j forAb2. Typically, the tether oligonucleotide of the antibody Ab1 differsfrom the tether oligonucleotide of the second antibody Ab2. In thiscase, a′ and j are not equivalent in sequence. Splint oligonucleotidesP1 and P2 each contain a sequence (optionally near the 5′ end) that iscomplementary to the oligonucleotide sequences a′ and j. For example, P1contains sequence a, and P2 contains sequence j′. Sequence a of probe P1hybridizes to sequence a′ of Ab1, and sequence j of Ab2 hybridizes tosequence j′ of P2. In this embodiment, P1 and P2 each contain a short 3′sequence that is complementary to the other probe; therefore, sequence(e f) of P1 is complementary to (f′ e′) of P2. Appreciable hybridizationof these complementary 3′ sequences of P1 and P2 occurs with highefficiency only when the probes P1 and P2 are brought into spatialproximity by consequence of also being hybridized to tetheroligonucleotides (a′ and j) of the antibodies bound to proximateepitopes. Hybridization of the 3′ ends of P1 and P2 creates a shortduplex with recessed 3′ ends, which may then be extended by polymerase.In one embodiment, extension of the 3′ ends serves to displace thesplint oligonucleotides P1 and P2 from the tether oligonucleotides (andantibodies), while simultaneously creating a duplex comprised of theextension products (P1-ext and P2-ext) of both probes (FIG. 3F). P1 andP2 extension products may then be detected by a variety of amplificationmethods known in the art, including PCR, SDA, ligase chain reaction,3SR, Qβ replicase-based amplification, solid phase amplification andNASBA. Sequences contained on the probes, e.g., sequences (b, c, d, e,f) of P1, and (e′, f′, g′, h′, i′, j′) of P2, or probe extensionproducts may be used to facilitate amplification and detection of theprobes. Special sequences that may be used to facilitate amplificationinclude primer binding sites, restriction endonuclease sites, sequencescapable of hybridizing with hybridization blocker oligonucleotides, RNApromoter sites, and the like. Detection of amplified products may occurby heterogeneous or homogeneous methods well-known in the art.Alternatively, duplex II of FIG. 3F may be detected directly withoutamplification by methods well-known in the art. If the method employs aDNA polymerase that possesses a 5′-3′ exonuclease activity, e.g., TaqDNA polymerase, the tether oligonucleotide (a′ or j) may be degradedduring the extension process, and the degradation products may bedetected as an indication of the presence of target antigen.

While FIGS. 3E and 3F depict antibodies conjugated to the 3′ ends of thetether oligonucleotides, FIG. 3H depicts alternative configurations inwhich both antibodies of a proximity pair are conjugated to the 5′ endsof the tether oligonucleotides. Likewise, FIG. 3I depicts an embodimentin which one tether oligonucleotide is conjugated to an antibody througha 5′ linkage and the other oligonucleotide is conjugated through a 3′linkage. In each of these latter two configurations, 3′ extension of theprobe sequences P1 and P2 results in displacement of the probes from thetether oligonucleotides and creation of a double-stranded duplexidentical to that shown in FIG. 3F.

If the tether oligonucleotides are not degraded during the displacementprocess, second set of probe molecules P1 and P2 may hybridize to thevacated tether oligonucleotides of the target-bound proximity members(FIG. 3G). As before, the 3′ ends of P1 and P2 anneal, and extensionagain results in displacement of the probes and creation of a duplexcomprised of P1-ext and P2-ext. The vacated tether oligonucleotidesagain anneal to a new pair of unextended probes (P1 and P2) if present,and the cycle of 3′ hybridization, extension, displacement, andsubsequent binding of unextended probes continues as long as Ab1 and Ab2remain bound to the proximate epitopes and a supply of P1 and P2 exists.As a result of this cycling process, multiple copies of detectable probeextension duplexes are formed from each target present.

In all the examples shown in FIGS. 3A-3L, initial hybridization of theprobes to the tether oligonucleotides may occur either before or afterthe antibody has bound to the target molecule, depending on theexperimental protocol used. In one embodiment, at least one of theantibodies Ab1 and Ab2 is or may be covalently or non-covalently linkedto a paramagnetic particle (FIG. 9) or other solid surface (FIG. 3L),e.g., the inner wall of a microwell. In configurations where at leastone of the antibodies is linked to a bead, solid surface or other solidmatrix, and both probes P1 and P2 (FIG. 3L) are attached indirectly tothe antibodies by hybridization to tether oligonucleotides, extension ofthe probes creates a duplex that is displaced from the antibody-targetcomplex, while the complex itself remains attached to the bead, solidsurface or other solid matrix. If desired, the solution containing thedisplaced duplex then may be removed and analyzed or amplified in aseparate well or compartment, leaving behind the complex and anymaterial bound non-specifically to the matrix surface.

In another embodiment of the present invention, a ligation splintoligonucleotide may be complementary to a portion of both splintoligonucleotides P1 and P2 as shown, for example, in FIG. 3J. Whenhybridized to the ligation splint oligonucleotide, probes P1 and P2 maybe ligated as described in FIG. 2 so that the 3′ end of P1 is covalentlyjoined to the 5′ end of P2 (FIG. 3J), which may then be amplified asdescribed in FIG. 2.

In an alternative embodiment, the splint oligonucleotide hybridizes to atether oligonucleotide (j′) and to one probe molecule P2, as exemplifiedin FIG. 3K. The 3′ end of the splint-bound P2 may then hybridize withthe complementary 3′ end of spatially proximate P1. 3′ extension of theprobes displaces the probes from the splint and tether oligonucleotidesand forms a full-length, amplifiable duplex analogous to that producedin the earlier examples shown in FIG. 3.

FIG. 4 shows hybridization blocker oligonucleotides that are designed toreduce the prevalence of hybridization between probe molecules linked toantibodies that are not bound to proximate epitopes. Suchtarget-independent hybridization is a source of background signalbecause it results in probe extension products that areindistinguishable from those produce by bona fide target binding events,and background signal reduces the overall sensitivity of the detectionmethod. The current invention comprises the use of hybridization blockeroligonucleotides (or “hybridization blockers”) to reduce spurious,target-independent probe interactions that lead to background signal.FIG. 4A depicts the basic principle underlying the use of hybridizationblockers in proximity-based amplification methods. Short sequences ofmutual complementarity (e f and f′ e′) (read 5′ to 3′) comprise the 3′ends of P1 and P2. These sequences may hybridize to each other to form aduplex with 5′ overhangs as shown. The number of probe moleculespopulating the duplexed versus single-stranded state depends on thetotal probe concentration and on the intrinsic stability of the duplex,which in turn is related to duplex length and composition. Theinteraction between P1 and P2 can be diminished or reversed by theaddition of a hybridization blocker oligonucleotide, preferably in molarexcess over the probes, which upon hybridization to P1 competitivelyblocks the interaction between the two probes. The blocker need not becomplementary to P1 across the entire subsequence that interacts withP2. Partial complementarity across this site also diminisheshybridization of P1 to P2.

In one embodiment, the hybridization blocker oligonucleotide comprises afirst subsequence (e′ or f′ e′) that is identical to part or all of thatportion of P2 that is complementary with P1 (subsequence e f). In asecond embodiment (FIG. 4B), the hybridization blocker oligonucleotidecomprises the first subsequence, defined above, and a second subsequence(d′ in FIG. 4B) that is complementary to a segment of P1, but notidentical to a subsequence of P2. The second subsequence of thehybridization blocker stabilizes the blocker-P1 interaction relative tothe P1-P2 interaction, thereby improving blocking efficiency. The secondsubsequence also may serve as a site for nucleation of the P1-blockerduplex in the event that P2 molecule is already hybridized to P1.Following nucleation, formation of the full P1-blocker duplex thendisplaces P2 from P1. The P1 subsequence d of this embodiment may bedirectly adjacent to the probe subsequence e, as shown in FIG. 4B, or itmay be located some nucleotides away from subsequence e (not shown). Inthe latter case, the hybridization blocker subsequence d′ may be linkedindirectly to hybridization blocker subsequence e′ through a spacer,comprising additional nucleotides and/or a non-nucleotide linker, suchas a tetraethylene glycol (TEG) moiety.

In a third embodiment (FIG. 4C), the hybridization blockeroligonucleotide may comprise a first subsequence (defined above),optionally a second subsequence (defined above), and a third subsequence(t′ s′ in FIG. 4C), which is located 5′ of the first subsequence andwhich may serve as a template for the 3′ extension of P1. The thirdsubsequence optionally may contain a suitable non-nucleotide moiety m′(i.e., a “5′ cap”), which are well known in the art, to prevent theaddition of non-templated nucleotides to the 3′ extension product of P1and to discourage binding of polymerase to the blunt-ended duplex formedby extension of P1 (see FIG. 4C). Preferably, the 3′ extension of P1 onthe blocker-template yields a P1-extension product containing a newsequence (s t) at its 3′ end that is not complementary to the P2sequence. Addition of the 3′ sequence (s t), therefore, serves todisable P1 as a functioning primer for DNA synthesis on a P2 template.Addition of the sequence (s t) also serves to stabilize the blocker-P1interaction by increasing the number of complementary base pairs betweenthe two molecules. Optionally, the new 3′ sequence (s t) produced inthis embodiment is entirely or partially complementary to a segment ofP1, such that, if the extended P1 and hybridization blocker dissociate,the extended P1 will fold into a stem-loop (hairpin) structure,diminishing any interaction with P2. In this case, the 3′ end of the P1hairpin optionally may be extended to lengthen the stem of the hairpin,and this extension optionally may create a nickable or cleavablerestriction endonuclease site within the P1 molecule.

In a fourth embodiment, it may be desirable to block reversibly theinteraction between P1 and P2 during a certain phase of a process. FIG.4D depicts a hybridization blocker design that allows reversibleblocking. In this embodiment, the hybridization blocker comprises asubsequence (e′ d′) that is complementary to the probe to be blocked (P1in FIG. 4D) and one or more tail sequences (t′ and/or k′) that are notcomplementary to the probe. Hybridization of the hybridization blockerto P1 precludes P1-P2 interactions. At the desired time, a deblockingoligonucleotide may be added to displace the hybridization blockeroligonucleotide from P1, freeing the latter to interact with P2. Thedeblocking oligonucleotide comprises one or more tail sequences (tand/or k) that are complementary to the tail sequences of thehybridization blocker. The tail sequences serve as a site of nucleationfor the blocker-deblocker hybridization. Once hybridization of thecomplementary tail sequences is nucleated, additional base-pairs formbetween the hybridization blocker and deblocker until the blocker isdisplaced from P1. To ensure displacement of the blocker from the probe,the overall thermodynamic stability of the blocker-deblocker complexmust be higher than the probe-blocker complex. The deblockingoligonucleotide need not be perfectly complementary to the hybridizationblocker oligonucleotide, provided that the thermodynamic stability ofthe blocker-deblocker duplex is higher than the stability ofprobe-blocker duplex. For instance, it may be desirable for thedeblocker to contain one or more nucleotides that form mismatches withthe hybridization blocker oligonucleotide, provided that the resultingblocker-deblocker duplex is more stable than the probe-blocker duplex.In particular, it may be desirable for sequence e of the deblocker tocontain one or more nucleotides that form one or more mismatches withsequence e′ of the blocker. The primary function of these mismatchingnucleotides of the deblocker is to destabilize potential interactionsbetween sequence e of the deblocker and sequence e′ of P2. In avariation of this embodiment, the hybridization blocker may be displacedby polymerase-catalyzed extension of sequence k as shown in FIG. 4E. Inthis case, the deblocking sequence is synthesized directly upon theblocking sequence, and no separate deblocker oligonucleotide need beadded. In yet another embodiment, a probe may comprise a 3′ stem-loopstructure at or near its 3′ end that serves to, block interactionsbetween probe molecules (see FIG. 11).

To prevent 3′ extension of the blocker by polymerase, all hybridizationblocker oligonucleotides described above, except the hybridizationblocker with the hairpin structure depicted in FIG. 4E, may comprise acap on the 3′ terminal nucleotide. Hybridization blockeroligonucleotides with 3′ caps are referred to as “cappedoligonucleotides.” Such 3′ caps are well-known in the art and includeinverted nucleotides, 2′-3′ dideoxyribonucleotides, and 3′deoxyribonucleotides. Hybridization blocker oligonucleotides may containa 3′ tail sequence that does not form complementary base-pairs with theprobe nucleotides when the hybridization blocker forms a duplex with theprobe. The non-base-paired 3′ tail also serves to prevent 3′ extensionof the blocker when the hybridization blocker is duplexed with the probeand, therefore, serves as a “3′ cap” as well.

FIG. 4EE illustrates the use of a 3′ tail on Probe 1 (P1) to facilitatestabilization of the P1 blocker duplex. The 3′ tail of P1 is comprisedof sequence x y and is located 3′ of sequence (e f), which is capable ofhybridizing with sequence (f′ e′) of Probe 2 (P2). The 3′ tail of P1does not hybridize to P2. The hybridization blocker comprises sequence(y′ x′ f′) and optionally e′. The hybridization blocker is, therefore,capable of hybridizing to P1 to form a duplex covering the 3′ tail ofP1, as well as all or part of sequence e f of P1. Formation of theblocker:P1 duplex will reduce the prevalence of P1:P2 hybrids asdescribed above. Base-pairing between (x y) of P1 and (y′ x′) of thehybridization blocker serves to stabilize the blocker:P1 duplex. Thehybridization blocker optionally comprises sequence z′ located 5′ ofsequence (y′ x′). Sequence z′ may serve as a site for initiatinghybridization of the deblocker oligonucleotides in methods describedabove.

FIG. 4F illustrates the use of hybridization blocker oligonucleotides ina binary immuno-amplification reaction. P1 and P2 are conjugateddirectly to antibodies Ab1 and Ab2, respectively. The same principlesapply regardless if the probes are bound to an antibody indirectly viahybridization to a tether oligonucleotide, or if the analyte-specificbinding components are aptamers or other analyte-specific bindingmolecules other than antibodies. As depicted, a hybridization blockeroligonucleotide hybridizes to the 3′ end of P1, precluding itsinteraction with P2. Hybridization of the hybridization blocker does notinterfere with binding of the antibody to the target analyte, andinitially the hybridization blocker is hybridized to P1 strands whetheror not Ab1 is complexed with the analyte or free in solution (state I).Typically, the concentration of free Ab1 and Ab2 (and the conjugatedprobes) in bulk solution is between 1 fM and 10 nM. Becausehybridization blocker concentrations typically are 10- to 100,000-foldhigher than probe concentrations, blocker-P1 interactions predominateover P1-P2 interactions for probes that are conjugated to antibodiesthat are not target-bound; however, when epitopes 1 and 2 of a targetmolecule are bound to Ab1 and Ab2, respectively, the effective localconcentration of P1 relative to P2 on the ternary target-antibodycomplex becomes much higher (typically 1-100 μM) than the concentrationof probes and hybridization blockers in bulk solution. As a result, theP1:P2 duplex prevails over the P1:blocker duplex for probes linked totarget-bound antibodies (state II). Polymerase-catalyzed extension ofthe 3′ ends of the P1:P2 hybrids, therefore, results in an amplifiableduplex on the target-Ab1-Ab2 complex (state III), while probes notlinked to target complexes remain blocked, unextended and incapable ofbeing amplified. While FIG. 4F depicts the use of a single hybridizationblocker that hybridizes with only one of the probes, a secondhybridization blocker that hybridizes with the other probe may be usedin conjunction with the first blocker.

FIG. 4G depicts a similar reaction scheme, employing hybridizationblockers capable of “disabling” P1 molecules by functioning as atemplate for extension (see FIG. 4C above). For the reasons set forthabove, the blocker:P1 duplex predominates over the P1:P2 duplex forprobes in bulk solution, whereas the P1:P2 duplex prevails on theternary, target-antibody complex. Polymerase-catalyzed extension of theblocker:P1 duplex results in a “disabled” P1 extension product (see FIG.4C), while extension of the of the P1:P2 duplex results in anamplifiable duplex as in FIG. 4F.

FIG. 4H depicts a step-wise blocking process, in which a displaceablehybridization blocker A hybridizes to P2, forming a blocker A:P2 duplex.Optionally, hybridization blocker A in this scheme may have a sufficientlength or concentration to make the blocker A:P2 duplex more stable thanthe P1:P2 duplex, both in bulk solution and on the ternary,target-Ab1-Ab2 complex. A second hybridization blocker B that iscomplementary to a segment of P1 and a deblocker D that is complementaryto displaceable hybridization blocker A are added to the solution,resulting in displacement of A from P2, formation of P1:blocker Bduplexes in bulk solution, and formation of P1:P2 duplexes on theternary, target-antibody complex. Optionally, hybridization blocker Bmay comprise a “disabling” sequence to disable P1 as described above(see FIGS. 4C and 4F). As before, polymerase-catalyzed extension of theprobe-probe hybrid results in an amplifiable duplex, while optionalextension of the P1:blocker B duplexes results in a “disabled” P1extension product.

FIG. 4I depicts a reaction scheme in which the P1:P2 duplex is allowedto form both in bulk solution and on the ternary, target-antibodycomplex. Addition of a hybridization blocker then preferentiallydisrupts P1:P2 duplexes in bulk solution compared to those on theternary target complex because of the different effective probeconcentration in bulk solution versus the ternary complex (see FIG. 4F).

In one embodiment, the hybridization blocker oligonucleotide may becovalently or non-covalently linked to a paramagnetic particle or othersolid surface and further may be used to reversibly bind proximitymembers to the surface (see FIG. 6). In another embodiment of thepresent invention, at least one of the antibodies Ab1 and Ab2 is, or maybe, covalently or non-covalently linked to a paramagnetic particle (seeFIG. 9) or other solid surface.

The embodiment of the present invention depicted in FIG. 5 comprises asplint oligonucleotide that is designed to bridge the gap between twoproximity members. In one embodiment, the splint oligonucleotide Scomprises an RNA polymerase promoter sequence, a downstream primerbinding sequence, and a detector region (FIG. 5A). The 5′ sequence ofsplint S is complementary to the 5′ end of P1, which is conjugated toantibody Ab1 at its 3′ terminus. In addition, the 3′ sequence of splintS is complementary to the 3′ end of probe P2, which is conjugated toantibody Ab2 at its 5′ end. When antibodies Ab1 and Ab2 are bound totheir respective epitopes, splint oligonucleotide S is able to hybridizeto both P1 and P2 (FIG. 5A). Extension from the 3′ ends of probe P2 andsplint S displaces probe P1 and creates a double-stranded moleculelinked to antibody Ab2, which possesses a functional RNA polymerasepromoter (FIG. 5B). RNA polymerase produces single-stranded RNAs, usingthis double-stranded promoter sequence. In one embodiment (not shown),the single-stranded oligonucleotides are detected directly by anysuitable method known in the art. In a second embodiment, thesingle-stranded RNA molecules hybridize to complementary primers that inturn are extended to generate DNA:RNA hybrids (FIG. 5C). Digestion ofthe RNA strand of these hybrids with an RNase produces single-strandedDNA molecules to which primers containing an RNA polymerase promoter mayhybridize (FIG. 5D). Extension from the 3′ ends of the hybridizedprimers and their target strands generates double-stranded RNApolymerase promoter sequences, leading to exponential amplification.

Another aspect of the present invention, illustrated in FIG. 6,comprises different methods for attaching antibodies, antigens orantigen-antibody complexes to solid surfaces by oligonucleotidehybridization to a capture oligonucleotide that is attached directly toa support, which may be a solid surface, polymer, hydrogel, or othersurface. Suitable supports for the invention, such as a particle ormicrotiter well surface, are well-known in the art. Methods of stablyconjugating oligonucleotides to various supports are well-known in theart as well. The capture oligonucleotide may interact by hybridizationwith an oligonucleotide moiety or it may interact with anotheroligonucleotide that is conjugated to an analyte-binding moiety of aproximity member. The invention further comprises methods of selectivelyreleasing the captured molecules from the surfaces by a variety ofchemical, physical or enzymatic means.

As shown in FIG. 6A, the antibody, antigen or antibody-antigen complex Cmay be conjugated to P1 via its 5′ terminus. The conjugatedoligonucleotide comprises a restriction enzyme recognition sequence andoptional flanking sequences and hybridizes to a complementaryoligonucleotide P2, which is attached by its 5′ terminus to a solidsurface. Release of the complex C from the solid phase occurs throughthe specific activity of a restriction enzyme that cleaves thedouble-stranded recognition sequence formed by hybridization of P1 andP2. P1 in all the panels of FIG. 6 may be the amplifiableoligonucleotide moiety of the proximity member (see FIG. 6N), or it maybe another oligonucleotide that is conjugated to the analyte-specificbinding moiety.

As shown in FIG. 6B, the antibody, antigen or antibody-antigen complex Cmay be conjugated to P1 via its 5′ terminus. The conjugatedoligonucleotide comprises a restriction enzyme recognition sequence andoptional flanking sequences and hybridizes to a complementaryoligonucleotide P2 attached by its 5′ terminus to a solid surface. P2comprises the complement of oligonucleotide P1 and a 3′non-complementary tail. Release of complex C from the solid phase occursthrough the specific activity of a restriction enzyme that cleaves thedouble-stranded recognition sequence formed upon hybridization ofoligonucleotides P1 and P2. The cleaved P1 oligonucleotide is renderedsingle-stranded through hybridization of the displacementoligonucleotide D.

As shown in FIG. 6C, the antibody, antigen or antibody-antigen complex Cmay be conjugated to P1 via its 3′ terminus. The conjugatedoligonucleotide comprises a restriction enzyme recognition sequence andoptional flanking sequences and hybridizes to a complementaryoligonucleotide P2 attached by its 3′ terminus to a solid surface.Release of the complex C from the solid phase occurs through thespecific activity of a restriction enzyme that cleaves thedouble-stranded recognition sequence formed upon hybridization of P1 andP2.

As shown in FIG. 6D, the antibody, antigen or antibody-antigen complex Cis conjugated to P1 via its 5′ terminus. The conjugated oligonucleotidecomprises a sequence that is complementary to the 3′ end of anoligonucleotide P2 that is attached through its 5′ terminus to a solidsurface. P2 comprises a restriction enzyme recognition sequence andoptional flanking sequences. DNA polymerase extension from the 3′ end ofP1 results in synthesis of the complement of P2 and the formation of adouble-stranded restriction enzyme recognition sequence that may becleaved selectively to release complex C. In a further embodiment, the3′ end of oligonucleotide P2 may be capped to prevent extension.

As shown in FIG. 6E, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 5′ terminus. Theconjugated oligonucleotide comprises a restriction enzyme recognitionsequence together with optional flanking DNA and a sequence that iscomplementary to the 3′ end of an oligonucleotide P2, which is attachedthrough its 5′ terminus to a solid surface. DNA polymerase extensionfrom the 3′ end of P2 results in synthesis of the complement ofoligonucleotide P1 and formation of a double-stranded restriction enzymerecognition sequence that may be cleaved selectively to release complexC. In a further embodiment, the 3′ end of oligonucleotide P1 may becapped to prevent extension.

As shown in FIG. 6F, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 5′ terminus. Theconjugated oligonucleotide comprises a sequence that is complementary toanother oligonucleotide P2 that is attached by its 5′ terminus to asolid surface. Release of the complex C from the solid phase occursthrough a change in the physical environment such as a reduction inionic strength, the addition of chelating agent(s), a change in pH or anincrease in temperature or a combination of these factors. Underappropriate conditions, physical release of complex C is reversible.

As shown in FIG. 6G, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 5′ terminus. Theconjugated oligonucleotide comprises a sequence that is complementary toanother oligonucleotide P2, which is attached by its 5′ terminus to asolid surface. The sequence of P2 comprises at least a partialcomplement of P1 and a scissile linkage that may be cleaved by physical,chemical or photochemical means to release complex C into solution.Examples of scissile linkages include, but are not limited to, disulfidebonds (cleaved, for example, by DTT) and cis-hydroxyl groups (cleaved byperiodate). In FIG. 6GG, the probe P1 bearing antibody, antigen,antibody-antigen complex is attached to a solid-surface through ascissile linkage, e.g., disulfide, cis-glycol, etc. Physical, enzymatic,chemical or photochemical cleavage of linkage may be used to liberatethe P1-bearing complex from the surface.

As shown in FIG. 6H, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 5′ terminus. Theconjugated oligonucleotide comprises an optional 5′ sequence and 3′sequence a′. Oligonucleotide P2 is attached via its 5′ terminus to asolid support and comprises sequence a and upstream sequence b.Hybridization of a and a′ attaches complex C to the support. Selectiverelease of complex C is achieved through the addition of thedisplacement oligonucleotide D, which comprises sequences a′ and b′.Hybridization of D to sequences a and b of P2 is thermodynamicallyfavored over hybridization of sequences a and a′ alone, resulting indisplacement of P1 and release of complex C into solution. In a secondembodiment, the displacement probe may be complementary to all or partof P1. In a third embodiment, the antibody or antibody-antigen complexmay be linked to the surface-bound oligonucleotide P2 indirectly througha splint oligonucleotide (not shown), which comprises sequencescomplementary to both surface-bound oligonucleotide and the P1. In thislatter case, displacement may occur by hybridization of oligonucleotideD to either P1, P2, or the splint oligonucleotide.

As shown in FIG. 6I, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 5′ terminus. Theconjugated oligonucleotide comprises an optional 3′ sequence a′.Oligonucleotide P2 is attached via its 5′ terminus to a solid support,and P2 comprises sequence a and downstream sequence b. Hybridization ofsequence a of oligonucleotide P2 and sequence a′ of oligonucleotide P1attaches complex C to the surface. Selective release of complex C isachieved through the hybridization of the displacement oligonucleotideD, comprising sequence b′, to sequence b of P2 and extension ofoligonucleotide D from its 3′ end using a strand-displacing DNApolymerase. In a further embodiment, the polymerase used for theextension reaction may possess 5′-3′ exonuclease activity, whichdegrades sequence a′ of P1 and releases the hybridized P2oligonucleotide. In an alternative embodiment, P2 may comprise a 3′hairpin structure (FIG. 6M), so that extension of the 3′ end of thehairpin by polymerase results in displacement of P1. In this embodiment,displacement oligonucleotide D is not required. Optionally, a splintoligonucleotide may be used in the embodiments depicted by FIGS. 6I and6M.

As shown in FIG. 6J, the antibody, antigen or antibody-antigen complex Cis conjugated to an oligonucleotide P1 via its 3′ terminus. Theconjugated oligonucleotide comprises 3′ sequence b and 5′ sequence a.Oligonucleotide P2 is attached via its 3′ terminus to a solid supportand comprises sequence a′ and an optional downstream sequence.Hybridization of a of oligonucleotide P1 and a′ of oligonucleotide P2attaches complex C to the surface. Selective release of complex C isachieved through the hybridization of the displacement oligonucleotide Dto sequence b of P1 and extension from the 3′ end using a stranddisplacing DNA polymerase. In a further embodiment, the polymerase usedfor the extension reaction may possess 5′-3′ exonuclease activity, whichdegrades the sequence a′ of P2 and releases the hybridized P1oligonucleotide.

In FIG. 6K, the antibody, antigen or antibody-antigen complex C isconjugated to an oligonucleotide P1 via its 5′ terminus. The conjugatedoligonucleotide comprises an optional 5′ sequence b and a 3′ sequence a.Oligonucleotide P2 is made of RNA, is attached via its 5′ terminus to asolid support and comprises sequence a′. Hybridization of sequence a ofoligonucleotide P1 and sequence a′ of oligonucleotide P2 attachescomplex C to the surface. Release of complex C is achieved through theaddition of an RNase, such as RNase H, which selectively degrades theRNA strand of a DNA:RNA hybrid. In an alternative embodiment,conjugation of P1 to Ab1 and attachment of P2 to the solid supportoccurs via the 3′ terminus of the respective oligonucleotides.

In FIG. 6L, the antibody, antigen or antibody-antigen complex C isconjugated to an oligonucleotide P1 via its 5′ terminus. The conjugatedoligonucleotide is made of RNA and comprises an optional 5′ sequence band 3′ sequence a. Oligonucleotide P2 is attached via its 5′ terminus toa solid support and comprises sequence a′. Hybridization of sequence aof oligonucleotide P1 and sequence a′ of oligonucleotide P2 attachescomplex C to the surface. Release of complex C is achieved through theaddition of an RNase, such as RNase H, that selectively degrades the RNAstrand of the DNA:RNA hybrid. In an alternative embodiment, conjugationof P1 to Ab1 and attachment of P2 to the solid support occurs via the 3′terminus of the respective oligonucleotides.

In the embodiment illustrated by FIG. 6N, the immobilized proximitymember is released by cleavage with a restriction endonuclease. Ab1 isconjugated to an oligonucleotide P1 that comprises sequence (a b c).Antibody Ab2 is conjugated to oligonucleotide P2 that comprises thesequence (a′ b′ c′ d′ e′), where the region d corresponds to arestriction endonuclease recognition site. Antibody Ab2 is bound to itsspecific epitope, and the antibody-antigen complex is captured to asolid support by hybridization of oligonucleotide P2 to a complementarycapture oligonucleotide C, which is attached to the surface. The supportoptionally is washed to remove unbound antigen and other components ofthe sample. Antibody Ab1 is then added, whereupon it binds epitope 1.The degree of complementarity between oligonucleotide P2 and captureprobe C is greater than that between P2 and oligonucleotide P1;therefore, hybridization between P1 and capture probe C isthermodynamically favored over hybridization of oligonucleotides P1 andP2. The antigen-antibody complex is released upon cleavage of therestriction endonuclease recognition site d. The remaining fragment ofoligonucleotide P2, attached to antibody Ab2, comprises the sequence (a′b′ c′) and is complementary to probe P1 on antibody Ab1. Hybridizationof (a′ b′ c′) to its complement is thermodynamically favorable andresults in the linkage of antibodies Ab1 and Ab2 through anoligonucleotide hybrid with extendible 3′ ends. This complex may be usedin a suitable amplification reaction, such as that depicted in FIG. 1.

FIG. 7A shows immobilization of a proximity member through aninteraction of the oligonucleotide moiety with a captureoligonucleotide, where the oligonucleotide moiety is capable of formingan amplicon when the oligonucleotide moiety is released from the captureoligonucleotide. The capture oligonucleotide, comprising regions b, cand y, is shown conjugated to the solid support by its 5′ end, althoughit also may be attached via its 3′ end. Regions b and c interact byhybridization with regions b′ and c′, respectively, of anoligonucleotide moiety P1. Region y represents a site that promotesrelease by any of the methods described above, including those shown inFIGS. 6A-6N. Ab2 may be immobilized on the solid support before or afterit binds to the analyte Ag. FIG. 7B shows an embodiment in which Ab2 isimmobilized before Ab2 binds the analyte Ag. In one embodiment, thebound proximity member-analyte complex is washed prior to amplificationto reduce the background signal by removing unbound molecules. Thecomplete complex between Ab2, Ab1, and the target analyte is shown inFIG. 7C.

FIG. 7D illustrates what is believed to be a source oftarget-independent amplification arising through non-specificinteractions between two proximity members. As shown, this non-specificinteraction takes place between Ab1 and Ab2, although other sources ofnon-specific interactions are possible. The interaction between Ab1 andAb2 promotes the interaction of P1 and P2 via complementary regions, inthis case regions (d e) and (d′ e′), respectively, which are used toform the amplicon. Formation of the P1:P2 interaction likewise maypromote the continued association between Ab1 and Ab2; therefore,destabilization of the P1:P2 interaction may decrease the overalltarget-independent signal. This can be accomplished by providing ahybridization blocker oligonucleotide that interacts with region (d e)of P1, for example, to prevent the interaction of this region with itscomplement (d′ e′) in P2.

The use of a hybridization blocker oligonucleotide in a method to detectan analyte by amplification is illustrated in FIGS. 7E-7H. Ab2 is boundto epitope 2 of an analyte before the addition of Ab1 or simultaneouslywith the addition of Ab1 to the reaction mixture, and Ab2 is immobilizedto a surface by interaction with a capture oligonucleotide. The captureoligonucleotide in this embodiment hybridizes with region (b′ c′) of P2.Optionally, the bound complex is washed before or after complexformation between Ab2 and the analyte to remove unbound molecules. Ab1is added in the presence of a hybridization blocker oligonucleotidecomprising a region (d′ e′) that is hybridized with the region (d e) ofP1 to suppress the interaction of Ab1 and Ab2, as described above.Unbound Ab1 may be washed from the reaction vessel after Ab1 has formeda complex with epitope 1 of the analyte. As shown in FIGS. 7E-7H, thehybridization blocker oligonucleotide does not interfere with theformation of a target-specific complex. The release of P2 from thecapture oligonucleotide allows region (d′ e′) of P2 to interact withregion of (d e) of P1 to form a double-stranded initiation site foramplification. P2 may be released from the capture oligonucleotide byany of the means described above. For example, as depicted in FIG. 7I,P2 is released by changing the ionic strength of the buffer (see FIG.6F, which shows physical release from the capture oligonucleotide). Asshown in FIG. 7I, once P2 is released, it is free to interact with P1 toform a double-stranded sequence that may be amplified. Alternatively, adisplacement oligonucleotide may be used to dissociate P2 from thecapture oligonucleotide, along the lines shown in FIG. 7J (see also FIG.6H).

FIG. 7I illustrates how changes in ionic strength may be usedselectively to release P2 and promote the subsequent interaction of P1and P2. In FIG. 7I, the formation of a complex among Ab1-P1, Ab2-P2, anda target analyte is achieved in a buffer that may have an ionic strengthoptimal for the formation of the ternary complex. Unbound ornon-specifically bound Ab1-P1 may be washed away in a high-ionicstrength buffer, which weakens non-specific interactions but maintainsthe duplex formed between sequences (b′ c′) of P2 and the captureoligonucleotide, as well as the complex formed between Ab1, Ab2, and thetarget analyte. Shifting the ionic strength of the buffer to a low-ionicstrength has the effect of melting the duplex between P2 and the captureoligonucleotide. The degree of destabilization of a nucleic acid duplexby lowering ionic strength can be calculated for any sequence ofnucleotides using the methods set forth in Sambrook et al., MolecularCloning, A Laboratory Manual (3rd ed., 2001), for example. Shifting theionic strength back to high ionic strength after the complex isdissociated from the capture oligonucleotide allows P1 and P2 tohybridize to form an amplifiable sequence.

In FIG. 8A, antibodies Ab1 and Ab2 recognize adjacent antigenic epitopesand are conjugated via 5′ terminal linkages to oligonucleotides P1 andP2, respectively. The 3′ ends of P1 and P2 are complementary, andantibody Ab2 is also linked either covalently or non-covalently to aparamagnetic particle. Antibody Ab1 is allowed to bind to its specificepitope prior to addition of paramagnetic particles that are coated withAb2. Binding of Ab2 adjacent to Ab1 permits hybridization of the 3′ endsof oligonucleotides P1 and P2. The concentration of Ab1 and Ab2 insolution is low relative to that bound to the surface of the antigen,such that antigen-independent hybridization of P1 and P2 is minimized.The antibody-antigen complex is captured by application of a magneticfield, and unbound Ab1 antibody is removed by washing. The P1:P2 hybridmay then be used in a suitable amplification reaction, such as thatdepicted in FIG. 1.

In FIG. 8B, antibodies Ab1 and Ab2 recognize adjacent antigenic epitopesand are conjugated via 5′ terminal linkages to oligonucleotides P1 andP2, respectively. The 3′ ends of P1 and P2 are complementary, andantibody Ab1 is also linked either covalently or non-covalently to aparamagnetic particle. Antibody Ab1 is allowed to bind to its specificepitope prior to addition of antibody Ab2. Binding of Ab2 adjacent toAb1 permits hybridization of the 3′ ends of oligonucleotides P1 and P2.The concentration of Ab1 and Ab2 in solution is low relative to thatbound to the surface of the antigen, such that antigen-independenthybridization of P1 and P2 is minimized. The antibody-antigen complex iscaptured by application of a magnetic field, and unbound Ab2 antibody isremoved by washing. The P1:P2 hybrid may then be used in anamplification reaction.

In FIG. 8C, antibodies Ab1 and Ab2 recognize adjacent antigenic epitopesand are conjugated via 5′ terminal linkages to oligonucleotides P1 andP2, respectively. The 3′ ends of P1 and P2 are complementary, andantibody Ab1 is also linked either covalently or non-covalently to aparamagnetic particle. Both antibodies Ab1 and Ab2 are allowed to bindto their specific epitopes simultaneously. Binding of Ab2 adjacent toAb1 permits hybridization of the 3′ ends of oligonucleotides P1 and P2.The concentration of Ab1 and Ab2 in solution is low relative to thatbound to the surface of the antigen, such that antigen-independenthybridization of P1 and P2 is minimized. The antibody-antigen complex iscaptured by application of a magnetic field, and unbound Ab2 antibody isremoved by washing. The P1:P2 hybrid may then be used in anamplification reaction.

In FIG. 8D, antibody Ab2 bearing probe P2 is attached or attachable to asurface, e.g., a bead or a microwell wall, through a scissile linkage(see FIG. 6GG). Antibody Ab1 bearing P1 binds to epitope 1 of the targetantigen, and this complex is immobilized by binding of epitope 2 to thesurface-linked Ab1. Unbound Ab1 is washed away, and the scissile linkageis then cleaved, liberating the ternary complex from the surface. Thesolution phase containing the detached ternary complex is thentransferred to a second reaction well for amplification, leaving behindany Ab1 that is non-specifically bound to original surface.

Another aspect of the invention is illustrated in FIG. 9. Antibodies Ab1and Ab2 recognize adjacent antigenic epitopes. Oligonucleotide P1 isconjugated by its 3′ end to antibody Ab1. Oligonucleotide P2 isconjugated via its 5′ terminus to antibody Ab2. Antibody Ab1 is linkedeither covalently or non-covalently to a paramagnetic particle. The twoantibodies are mixed with the antigen and allowed to bind to theirrespective epitopes. The resulting antibody-antigen complex is capturedby the application of a magnetic field, and unbound Ab2 antibodies andother components of the sample matrix are removed by washing. Splintoligonucleotide S, which is complementary to the 5′ end of probe P1 andthe 3′ end of probe P2, is then added. Hybridization between the splintoligonucleotide S and the 5′ end of probe P1 and 3′ end of probe P2bridges the gap between the two antibodies. The P1:L:P2 hybrid then maybe used in an amplification reaction as depicted in FIG. 3. Other linkerconfigurations depicted in FIG. 3 may be used as well. In addition, Ab1may be attached to the paramagnetic or other particle through acleavable linkage as described in FIGS. 6A-6L.

Yet another aspect of the invention is set forth in FIG. 10. UnlabeledAb1 and Ab2 bind to proximate epitopes on the target antigen. Secondaryantibodies Sec1 and Sec2, e.g., anti-Fc1 and anti-Fc2, are labeledrespectively with oligonucleotide probes P1 and P2, which comprisemutually complementary 3′ ends. The secondary antibodies then bind tothe unlabeled primary antibodies Ab1 and Ab2, bringing theoligonucleotide probes into close proximity, whereupon hybridization andextension of the 3′ ends converts the probes into amplifiable strands.Optionally, Ab1 and Ab2 may be labeled with hapten moieties (e.g.,biotin, fluorescein, digoxigenin, trinitrophenol, dinitrophenol and thelike). In this case, probe-labeled secondary antibodies Sec1 and Sec 2possess binding specificities against the respective hapten labels ofAb1 and Ab2.

In a further embodiment, the secondary antibodies are labeled withprobes that can be ligated when mutually base-paired to a ligationsplint oligonucleotide (FIG. 2). When a pair of secondary antibodiesbinds to a pair of unlabeled antibodies that are bound to proximateepitopes, the probes mutually base-pair with the ligation splintoligonucleotide and ligation occurs.

In a third embodiment, the labeled secondary antibodies are combinedwith (and may bind to) the primary antibodies prior to or duringincubation with the antigen. In a fourth embodiment, at least one of thesecondary antibodies is linked to a solid surface, e.g., a microwellwall or a magnetic bead. In a fifth embodiment, the secondary antibodyis reversibly linked to a solid surface (FIGS. 6A-6L, 7A-7D, and 8A-8D).In a sixth embodiment, the surface-linked antibody is released from thesolid surface, and the released antibody is subjected to anamplification reaction. In a seventh embodiment, Ab1 and/or Ab2 may bean aptamer, receptor, or other epitope binding entity, and Sec1 and Sec2are probe-labeled recognition molecules that bind to Ab1 and Ab2. In aneight embodiment, the Sec1 and/or Sec2 may be a Fab′ fragment, anaptamer, an antibody against an antibody, or any molecule thatspecifically recognizes Ab1 or Ab2.

Protein G or Protein A optionally can be substituted for the Sec1 andSec2, as illustrated in FIG. 10. Protein G and Protein A bind to mostIgG molecules and to the Fc region, with one Protein G or Protein Abinding per IgG molecule. Specifically, Protein G or Protein A can bemodified with “universal oligonucleotide” probes (labeled P1 and P2 inFIG. 10). The modified Protein G molecules, for example, can bepre-bound to the antibodies that recognizing epitope 1 and epitope 2. Inthis case, Protein G or Protein A modified with P1 would be pre-bound toAb1. Likewise, Protein G or Protein A modified with P2 would bepre-bound to Ab2. Alternatively, the probe-modified Protein G or ProteinA molecules could be mixed together and used as depicted in FIG. 10.

This approach has certain advantages. First, only one reagent, namelyProtein G or Protein A, needs to be modified. Second, almost any primarydetector antibody can be used to attach to the antigen, e.g., a rat,mouse, or rabbit antibody. Third, pre-binding the modified Protein G orProtein A to the primary antibodies are specifically tagged reagentsavailable for general use with any Ab1 or Ab2. The resultingstandardization of the assay components is expected to improvequantification and reproducibility.

In some instances it may be advantages to use a Protein A/Protein Gfusion product in place of Protein A or Protein G. It should also beunderstood that “Protein A” or “Protein G” can refer to either thenatural bacterial product or to genetically engineered or recombinantversions that have been designed for optimal binding to the IgGmolecules, for example, by eliminating the albumin binding capability ofProtein G.

Another aspect of the present invention is shown in FIG. 11, in whichthe present invention comprises oligonucleotide-labeled antibodies foruse in immuno-amplification reactions that are precluded fromparticipation in non-specific primer-primer interactions through theincorporation of hairpin structures. Antibody Ab1 is conjugated tooligonucleotide P1, which comprises an SDA restriction enzyme nickingsite and a downstream sequence (a b a′ c), where a and a′ arecomplementary sequences that hybridize to form a hairpin structure. TheTm of the hairpin is sufficiently low so that a proportion of theoligonucleotide label exists in an open, relaxed form under theconditions of the amplification reaction. The T_(m) of a nucleic acidduplex can be calculated by methods well-known in the art for anysequence of nucleotides under a given set of temperatures and ionicstrengths, using one of the methods described in Sambrook et al.,Molecular Cloning, A Laboratory Manual (3rd ed., 2001), for example. The3′ terminal sequence c does not form part of the hairpin structure andis designed to prevent self-priming of DNA polymerase extension.Antibody Ab2 is conjugated to oligonucleotide P2, which comprises an SDArestriction enzyme nicking site and downstream sequence (a b′). Whenantibodies Ab1 and Ab2 bind to their respective epitopes, breathing ofthe hairpin of probe P1 permits base pairing to occur between the twooligonucleotide labels. The T_(m) of the P1:P2 hybrid formed by pairingof sequences (b a′) and (a b′) is greater than that of the P1 hairpin;therefore, hybridization of P1 and P2 is thermodynamically favored. DNApolymerase then extends the 3′ end of P2 to generate a double-strandedrestriction site that is capable of being nicked. Nicking, extension andstrand displacement leads to formation of a double-stranded DNA moleculewith nickable restriction sites at either end. This construct may beused in an exponential SDA reaction.

In another embodiment, antibody Ab1 may be conjugated to oligonucleotideP1, which comprises an SDA restriction enzyme nicking site anddownstream sequence (b′ a b a′ c), where a and a′ are complementarysequences that hybridize to form a hairpin structure. Sequences b and b′are also complementary, but they form a less stable structure than thatformed by hybridization of a and a′. Formation of the a:a′ hairpin is,therefore, favored. The 3′ terminal sequence c does not form part of thehairpin structure and is designed to prevent self priming of DNApolymerase extension. Antibody Ab2 is conjugated to oligonucleotide P2,which comprises sequence (b′ a′ b), where b and b′ are complementary andform a hairpin structure. Probe P2 lacks an SDA nicking site. Thus, ifDNA polymerase extension occurs from the 3′ end, a dead-end product isgenerated that cannot undergo linear amplification. The Tm of the a:a′and b:b′ hairpins is sufficiently low so that a proportion of eacholigonucleotide exists in an open, relaxed form under the conditions ofthe reaction. When antibodies Ab1 and Ab2 bind to their respectiveepitopes, breathing of the hairpins of probes P1 and P2 permits basepairing to occur between the two oligonucleotide labels. The Tm of theP1:P2 hybrid formed by pairing of sequences (b′ a b) and (b a′ b′) isgreater than that of the either hairpin structure; therefore,hybridization of P1 and P2 is thermodynamically favored. DNA polymerasethen extends the 3′ end of P2 to generate a nickable double-strandedrestriction site. Nicking, extension and strand displacement leads toformation of a double-stranded DNA molecule that may be fed into anexponential SDA reaction.

A further embodiment is depicted in FIG. 11C. Probe P1 comprises hairpinsequences b, d, b′, sequence a, which is 5′ of the hairpin sequences,and sequence c, which is 3′ of the hairpin sequences and whichoptionally contains a non-extendible 3′ cap. Sequences b and b′ arecomplementary and hybridize to form the stem of a hairpin structure.Sequence d forms the loop of the hairpin. Optionally, part of sequence dmay base pair with itself to form part of the stem structure along withb and b′. Probe P2 comprises sequence d′, which is complementary tosequence d of P1. The presence of the hairpin structure precludeshybridization of d and d′. Addition of a displacement oligonucleotide Dopens the hairpin by first hybridizing to sequence a of P1 andsubsequently displacing the b′ arm of the stem. Sequence d′ of P2 thenhybridizes with the unfolded sequence d of P1, and P2 is extended bypolymerase, displacing oligonucleotide D and creating a nickabledouble-stranded restriction site on P1. Amplification then follows in amanner analogous to the embodiment depicted in FIG. 11B.

FIG. 12 depicts a method for detecting the presence of antigen-specificimmunoglobulin antibodies in a test sample. Probes P1 and P2 areconjugated to an antigen molecule Ag, such that each Ag molecule islabeled with either P1 or P2, but not both. The labeled antigens aremixed with the test sample and bind to the Ag-specific immunoglobulin asshown. Complexes that contain both P1 and P2 will be amplifiable,detectable and indicative of the presence of an Ag-specificimmunoglobulin. In the absence of an Ag-specific immunoglobulin, nodetectable complex will form. A similar approach may be used to detectany ligand-receptor interaction comprising either two or more identicalligand binding sites or binding sites to two or more different ligands.In the latter case, each ligand is labeled with a different probesequence. For example, Protein G, which binds to the Fc region of IgG,may be labeled with P1, and Ag may be labeled with P2. Binding of thelabeled Ag and protein G to the same IgG molecule would create a complexthat is amplifiable and detectable by the methods of the presentinvention.

FIG. 13 shows representative probes, primers, adapters, reporters andtether oligonucleotides that are useful for binary immuno-SDA. Thestructure of these oligonucleotides and a method of their use is setforth in the following Examples. The following. Examples are in no wayintended to limit the scope of the invention.

Example 1 Representative Sequences of Probes, Primers, Adapters,Reporters Useful for Binary Immuno-SDA

The sequences of some of the probes, primers, adapters, and reportersshown below are set forth in FIG. 13.

Probes (P1, P2)

RHP-1 (right hand probe; sequence in bold is common with primer SRH-1,below):

(SEQ ID NO.: 1) 5′ CCA GTC TTG TCT TGT CTG TTC TCG GGA TGC ATTCAG TGA CGT GAT GAG CTA GAC AGA TGT ACA GT

RHP-3 (right hand probe; sequence in bold is common with primer SRH-1,below):

(SEQ ID NO.: 2) 5′ CCA GTC TTG TCT TGT CTG TTC TCG GGA TGC ATTCAG TGA CGT GAT GAG CTA GAC AGA TGT AC

RBD-3v3 (right hand probe; X=biotin-labeled dT; sequence in bold iscommon with primer SRH-1, below):

(SEQ ID NO.: 3) 5' CCA GTC TTG TCT TGT CTG TTC TCG GGA TGC ATTCAG TGA CGT GAT GAG CTA GAC AGA TGT AC TTT TXT

LHP-1 (left hand probe; underlined bases are complementary with the 3′end of RHP-1):

(SEQ ID NO.: 4) 5′ ATT CAC GCT TCC ATT CCA TGT CTC GGG TTTACT TCA TCT GCA ACT GTA C

LHP-2 (left hand probe; underlined bases are complementary with the 3′end of RHP-1):

(SEQ ID NO.: 5) 5′ ATT CAC GCT TCC ATT CCA TGT CTC GGG TTT ACTTCA TCT GCA ACT GTA CAT

LHP-3 (left hand probe; underlined bases are complementary with the 3′end of RHP-1):

(SEQ ID NO.: 6) 5′ ATT CAC GCT TCC ATT CCA TGT CTC GGG TTT ACTTCA TCT GCA ACT GTA CAT CTG T

LHP-4 (left hand probe; underlined bases are complementary with the 3′end of RHP-1):

(SEQ ID NO.: 7) 5′ ATT CAC GCT TCC ATT CCA TGT CTC GGG TTT ACTTCA TCT GCA ACT GTA CAT CTG TCT

LHP-5 (left hand probe; underlined bases are complementary with the 3′end of RHP-1):

(SEQ ID NO.: 8) 5′ ATT CAC GCT TCC ATT CCA TGT CTC GGG TTT ACTTCA TCT GCA ACT GTA CAT CT

Primers

SRH-1 (right-hand primer; sequence in bold is common with RHP-1):

(SEQ ID NO.: 9) 5′ CGA TTC AGC TGC AGA CGA TCT CGG GAT GCA TTC AGT GAC

SLH-2 (left-hand primer; sequence in bold is common with LHP-1, 2, 3, 4and 5; underlined bases are complementarity with the 3′ end of RHP-1):

(SEQ ID NO.: 10) 5′ ACC GCA TCG AAT GAC TGT CTC GGG TTT ACT TCA TCT GCA AC

Adapters

ADR-2 (underlined bases are identical to the 3′ end of TBD10.2 [D/R]):

(SEQ ID NO.: 11) 5′ ACG TTA GCC ACC ATA CGG ATA GTG ACG TGA TGAGCT AGA C

ADR-5 (underlined bases are identical to the 3′ end of TBD10.2 [D/R]):

(SEQ ID NO.: 12) 5′ ACG TTA GCC ACC ATA CGG ATG ATG AGC TAG AC

ADR-8 (underlined bases are identical to the 3′ end of TBD10.2 [D/R]):

(SEQ ID NO.: 13) 5′ ACG TTA GCC ACC ATA CGG ATG TGA CGT GAT GAG C

ADIQS-1 (IQS adapter):

(SEQ ID NO.: 14) 5′ ACG TTA GCC ACC ATA CGG ATG ATG AGC ATC TG

ADQS-2 (adapter for IQS-2; underlined bases are identical to 3′ end ofaltD6.9(F/D)):

(SEQ ID NO.: 15) 5′ AGC TAT CCG CCA TAA GCC AT AC TCA GAG TGA TCA AGT

Reporters

TBD10.2 (D/R) (underlined bases are identical to the 5′ end of ADR-2 andADR-5):

(SEQ ID NO.: 16) 5′ (dabcyl)-TAG CGC CCG AGC GCT ACG TT(rox)A GCCACC ATA CGG AT

altD6.9 (F/D):

(SEQ ID NO.: 17) 5′ (fam)-AGT TGC CCC GAG GCA ACT(dabcyl) AGCTAT CCG CCA TAA GCC AT

Tether Oligonucleotides

RCP-1 (tether oligonucleotide; UPPER CASE bases are complementary to the5′ end of RHP-1):

(SEQ ID NO.: 18) 5′ CCG AGA ACA GAC AAG ACA AGA CTG Gat at

LCP-2 (tether oligonucleotide; UPPER CASE bases are complementary to the5′ end of LHP 1-5):

(SEQ ID NO.: 19) 5′ CGA GAC ATG GAA TGG AAG CGT GAA Ttt tt

LCP-4 (tether oligonucleotide; UPPER CASE bases are complementary to the5′ end of LHP 1-5):

(SEQ ID NO.: 20) 5′ t tta ttt tat CGA GAC ATG GAA TGG AAG CGT GAA T

Capture and Displacement Oligos

RCP-13v1 (capture oligonucleotide; UPPER CASE bases are complementary toa sequence near the 5′ end of RHP-3; underlined bases are complementaryto DO-13v1; X=tetra-ethylene glycol; Z=hexa-ethylene glycol; X is linkedto Z through a phosphodiester moiety; and Z is linked to the 5′ end ofthe oligonucleotide through a phosphodiester moiety):

(SEQ ID NO.: 21) 5′ biotin-X-Z-cct ggt acg agt ttc tat cct AA TGCATC aCG AGA ACA GAC AAG ACA AG t

DO-13v1 (displacement oligonucleotide [cap]=3′ deoxyruidine):

(SEQ ID NO.: 22) 5′ CTT GTC TTG TCT GTT CTC GTG ATG CAT TAG GAT AGAAAC TCG TAC CAG G-[cap] 3′

RCP-9v2.2 (capture oligonucleotide; UPPERCASE bases are complementary tobases near the 5′ end of RHP-3; underlined bases are complementary todisplacement oligo CMPR-9v2; X=tetra-ethylene glycol; Z=hexa-ethyleneglycol; X is linked to Z through a phosphodiester moiety; and Z islinked to the 5′ end of the oligonucleotide through a phosphodiestermoiety):

(SEQ ID NO.: 23) 5′ biotin-X-Z-t tta CAC TGA ATG CAT tCC tAG AACAGA CAA GAC AAG ACT ccg tgg cAg cgt

CMPR-9v2 (capture oligonucleotide; UPPER CASE bases are complementary tothe 5′ end of RHP-3; [cap]=3′ deoxyuridine):

(SEQ ID NO.: 24) 5′ ACG CTG CCA CGG AGT CTT GTC TTG TCT GTT CTtGGA ATG CAT TCA GT-[cap] 3′Blocking Oligonucleotides ([cap]=2′,3′ dideoxycytidine)

LBK-1 (UPPERCASE bases are complementary to 3′ end of LHP-3):

(SEQ ID NO.: 25) 5′ ACA GAT GTA CAG Taa ttt-[cap] 3′

RDB-3p5 (UPPER CASE bases are complementary to 3′ end of RHP-1;underlined bases are complementary to 3′ end of RHP-3):

(SEQ ID NO.: 26) 5′ cag ttc agc acA CTG TAC ATC TGT CTA GC aa- [cap] 3′

RDB-3p8 (UPPER CASE bases are complementary to 3′ end of RHP-1;underlined bases are complementary to 3′ end of RHP-3):

(SEQ ID NO.: 27) 5′ cag ttc agc acA CTG TAC ATC TGT CTA GCT CA aa-[cap]3′

RDB-3p10 (UPPER CASE bases are complementary to 3′ end of RHP-1;underlined bases are complementary to 3′ end of RHP-3):

(SEQ ID NO.: 28) 5′cag ttc agc acA CTG TAC ATC TG T CTA GCT CATCta-[cap] 3′

RDB-3z8 (UPPER CASE bases are complementary to 3′ end of RHP-3):

(SEQ ID NO.: 29) 5′ cag ttc agc ac aa GTA CAT CTG TCT AGC TCA aac-[cap]3′

RDB-3z0 (UPPER CASE bases are complementary to 3′ end of RHP-3):

(SEQ ID NO.: 30) 5′ cag ttc agc ac aa GTA CAT CTG T aac-[cap] 3′

Quantification Standards and Quality Control (“QC”) Nucleotides

LTAR-1 (QC oligonucleotide from Epoch Biosciences (Bothell, Wash.);underlined bases differ from IQS-1):

(SEQ ID NO.: 31) 5′ TTT TAC TTC ATC TGC AAC TGT ACA TCT GTC TAGCTC ATC ACG TCA CTG AAT GCA T

IQS-1 (internal quantification standard; underlined bases differ fromLTAR-1):

(SEQ ID NO.: 32) 5′ TT TAC TTC ATC TGC AAC ACA TGA TCT CAG ATGCTC ATC ACG TCA CTG AAT GCA TC

IQS-2 (internal quantification standard; lower case bases differ fromtarget-derived amplicon):

(SEQ ID NO.: 33) 5′ TTA CTT CAT CTG CAA C at ctg tca ctt gat cactct ga G TCA CTG AAT GCA TC

Example 2 Experimental Demonstration of Homogeneous Immuno-SDA

In the following series of experiments, the analyte-specific bindingmoieties of the proximity members were biotin moieties, and the chosentest analyte was streptavidin (“SA”). Biotin was linked to the 5′ end ofthe oligonucleotide moieties P1 (RHP-1) and P2 (LHP-1 or LHP-3). (SeeEXAMPLE 1, above.) P1 and P2 were each at 1 μM concentration and weremixed with 10 mM Tris-EDTA buffer and bovine serum albumin (BSA) andoptionally SA at 0.25 μM. After 10 minutes at room temperature, themixtures were serially diluted so that the final probe concentrationswere in the pM range. The diluted mixtures were then mixed with SDAprimers (SRH1, SLH2), an adapter (ADR-5), and a reporter probe(TBD10.2), and the mixtures were heated to 72° C. for 10 minutes. Thesamples were cooled to 52° C. and added to “amplification wells,”containing a dried cocktail of SDA components that included dNTPs. Finalprobe concentrations were either 1 fM or 10 fM, and final SAconcentration was either zero or one-half the respective probeconcentrations. BsoBI restriction endonuclease and Bst DNA polymerase(BD Diagnostic Systems, Baltimore, Md.) were then added to the mixtures,and isothermal amplification was carried out for 1 hour at 52° C.Amplification was monitored by observing the fluorescence increaseassociated with conversion of the fluorescein-labeled reporter probe,TBD10.2, as described in U.S. Pat. No. 6,316,200.

MOTA values (a measure of fluorescence intensity integrated over thecourse of the 1 hour reaction) are reported in TABLE 1. When P2 isLHP-3, which forms a 13 bp duplex when hybridized to P1 (RHP-1), MOTAvalues are 100-1000-fold higher for samples containing the analyte SAthan for the controls that did not contain SA, demonstrating the abilityof this SDA-based binary probe system to detect the SA protein at sub-fMconcentration.

TABLE 1 Streptavidin 0 2.5 fM 0 0.25 fM 0 0.025 fM Concentration of eachRHP-1 and LHP-3 (13 bp overlap) 10 fM 10 fM 1 fM 1 fM 0.1 fM 0.1 fM MOTA300 198,090 0 161,570 10 10 Score 320 136,430 80 109,990 0 32,880 0166,240 630 146,010 0 86,240 30 171,020 890 157,530 0 71,780 0 154,760150 114,840 330 350 150 143,390 160 135,800 160 0 Mean 133 161,655 318137,623 83 31,877 % Control 111% 14% 112% 16% 164% 122% 0 2.5 fM 0 0.25fM Concentration of each RHP-1 and LHP-3 (7 bp overlap) 10 fM 10 fM 1 fM1 fM MOTA 1,830 170 80 10 Score 8,680 0 990 70 20 180 430 140 110 1205,680 0 100 320 990 10 12,870 10 140 10 Mean 3,935 133 1,385 40 %Control 140% 90% 155% 138%

Example 3 Experimental Demonstration of Heterogeneous Immuno-SDA

In this experiment, RHP-1, bearing either a 5′ biotin or a 5′aminolinker and no biotin, served as P1. LHP-1, bearing either a 5′biotin or a 5′ amino linker and no biotin, served as P2. 100 nM probeswere mixed with SA-coated beads (Promega, Madison, Wis.) and incubatedwith occasional agitation for 45 minutes at room temperature. The beadswere then gathered to the sides of the tube, and the solution wasremoved. The beads were resuspended in 0.1 mg/mL BSA before gatheringthem to the side of the tube and discarding the solution phase. Thesewashing steps were repeated four times before the beads were finallyresuspended in SDA reaction buffer. The resulting suspension was addedto a mixture containing SDA primers (SLH-2, SRH-1), an adapter (ADR-5),and reporter (TBD.10.2). Final concentrations of bead-bound SA in thesemixtures was 40 or 400 fM. SDA was then carried out as described inEXAMPLE 2, above.

The results are shown in TABLE 2. As expected, strong MOTA values wereobserved for reactions containing biotinylated probes and SA at either40 or 400 fM, indicative of conversion of SA-bound probes intoamplifiable extension products. By contrast, MOTA values were very lowfor control reactions containing SA and probes that were labeled with 5′aminolink groups instead of biotin. As expected for these controlreactions, the probes lacking biotin were unable to bind to thebead-linked SA and were consequently eliminated during the wash stepsand, therefore, were not converted to amplifiable extension products.The low signal that appears in the control reactions may result fromnon-specific binding of aminolinked probes to the bead surface.

TABLE 2 Biotin Probes Amino-Linked Probes [SA] 400 fM 40 fM 400 fM 40 fMMOTA 103,550 47,240 420 450 Score 115,900 970 0 0  91,580 0 250 40105,410 8,890 0 90    −47* 20,040 370 310  91,310 49,910 8,510 0 Mean101,550 21,175 1,592 148 No No Probes Probes [SA] 400 fM 40 fM No SAMOTA 120 110 160 Score  0 310 540 200 0 250 120 410 0  −45* 270 50 230380 1,430 Mean 134 247 405

Example 4 Experimental Demonstration of Immuno-SDA with a Single TetherOligonucleotide

In this experiment, un-biotinylated RHP-1 (see above) served as P1,LHP-3 (bearing a 5′ biotin) served as P2, and RCP-1 (bearing a 3′biotin) served as a tether oligo, TO. Probes P1 and P2 and tether oligoTO were mixed in equimolar ratios and added to tubes that eithercontained or lacked SA. The tubes were incubated briefly at roomtemperature, and the contents of the tube were then serially diluted togive probe concentrations in the pM range. The diluted mixtures werethen mixed with SDA primers (SRH1, SLH2), an adapter (ADR-5) and areporter probe (TBB10.2) for a final concentration of SA of either 0 or0.25 fM and a concentration of 1 fM each for P1, P2 and TO. The mixtureswere then either subjected to a “heat-spike” (72° C. for 10 minutes) orincubated at 52° C. for 10 minutes (“no heat spike”). The P1:TO duplex,which has an estimated T_(m) of 64° C., is expected to be stable at 52°C. and disrupted by incubation at 72° C. Upon disruption, the P1:TOduplex will reform only very slowly (t_(1/2)>100 hours) at the diluted(1 fM) probe concentrations. The samples were subjected to SDA byaddition of BsoBI restriction endonuclease, Bst DNA polymerase and adried cocktail of dNTPs, followed by incubation at 52° C. in a ProbeTec™ET instrument. When probes P1 and P2 are bound through TO or biotin,respectively, to a common SA molecule, their complementary 3′ endshybridize and are extended, creating hybridization sites for the SDAprimers (SLH-2 and SRH-1) and adapter ADR-5. This enables simultaneousamplification and detection of the extended P1 and P2 molecules.Amplification was monitored by observing the adapter-mediatedfluorescence increase associated with conversion of thefluorescein-labeled reporter probe, TBD10.2 (see U.S. Pat. No. 6,316,200for details of adapter mediated reporter probe conversion).

The results are shown in TABLE 3. “No heat spike” samples that containedthe analyte 0.25 fM SA and 1 fM probes showed a strong increase influorescence (average MOTA=166,000), while control samples lacking SAbut containing 1 fM probes displayed average MOTA values of just 3,000,which is comparable to values obtained from samples in which the P1:TOduplex was disrupted by the 72° C. heat spike prior to SDA. In sampleslacking SA, MOTA values remain low because formation of a P1-P2 duplexdoes not occur with appreciable efficiency at 1 fM probe concentration.

TABLE 3 Heat Spike No Heat Spike NO SA SA No SA SA 290 50 4740 17723022360 250 20 168210 30 380 1660 175550 MOTA {open oversize brace} 190210 8240 193620 27730 8100 350 139080 160 60 1500 145330 MEAN 10120 17983002 166503 % CV 136% 196% 116% 12%

Example 5 Analyte Quantification by Binary Immuno-SDA

Levels of target analyte in a sample may be determined quantitatively byincluding an internal standard (e.g., IQS-1 of EXAMPLE 1), which isco-amplified with target-mediated probe extension products. The internalstandard and target-dependent probe-extension products are amplified bycommon pairs of SDA primers but are detected by different anddistinguishably labeled reporter probes (e.g., TBD10.2 and AltD6.9 ofEXAMPLE 1). By comparing the relative signals of the two reporterprobes, one can deduce the concentration of the probe-specific extensionproducts relative to the known quantity of internal standard. Indetermining absolute concentrations of analyte, it may be advantageousto produce a “standard curve” of the ratio of background-correctedtarget/control signals versus target analyte signals. The ratio ofsignals observed for the test sample may then be compared against thestandard curve to produce absolute analyte concentration. Similarmethods of quantifying nucleic acid target levels are known in the art(see, e.g., Nadeau et al., “Real-time Sequence-specific Detection ofNucleic Acids during Strand Displacement Amplification,” Anal. Biochem.276: 177-187 (1999)).

Example 6 Experimental Demonstration of Immuno-SDA with Two TetherOligonucleotides

In this experiment, unbiotinylated RHP-1 (see above) served as P1, andunbiotinylated LHP-3 served as P2, while RCP-1 (bearing a 3′ biotin) andLCP-4 (bearing a 5′ biotin) served as tether oligonucleotides. Theinteraction between P1, P2 and the t ether oligonucleotides is showndiagrammatically in FIG. 3H. Probes P1 and P2 and tetheroligonucleotides were mixed in equimolar ratios (where the molarity wasdetermined with respect to only the tether oligonucleotide moieties ofthe proximity members) and added to tubes that either contained orlacked SA. Reactions were carried out as described in EXAMPLE 4, exceptno 72° C. “heat spike” experiment was performed. The results are shownin TABLE 4. Samples containing SA showed strong fluorescence increases(average MOTA values=136,000), while samples lacking SA displayednegligible increases (MOTA=533).

TABLE 4 NO SA SA 680 156740 470 138080 260 133150 MOTA {open oversizebrace} 200 137820 1200 127070 390 126840 MEAN 533 136617 % CV 69% 8%

Example 7 Experimental Demonstration of Homogeneous Immuno-SDA with IL-8as the Analyte

MAb G265-8 (Ab1; BD Bioscience Pharmingen), directed against human IL-8,was covalently coupled to SA to yield an anti-IL-8 IgG-SA conjugate(Ab1-SA) containing one SA moiety per IgG. MAb G265-8 and SA wereconjugated using methods well-known in the art. A mixture containing 20nM 5′ biotin-labeled probe RHP-3 (P1), 10 nM Ab1-SA conjugate, 10 nMTris-EDTA buffer, and 0.1 mg/ml BSA was prepared and incubated overnightat 4° C. to permit the biotinylated oligonucleotide to bind the Ab1-SAconjugate to form Ab1-SA-P1.

MAb G265-5 (Ab2; BD Bioscience Pharmingen), which binds an IL-8 epitopedistinct from that of MAb G265-8, was covalently coupled directly to anamino-modified form of probe LHP-3 (P2) to produce Ab2-P2 conjugateshaving an average of 2.5 P2 moieties per Ab2. MAb G265-5 and LHP-3 wereconjugated essentially as described in U.S. Pat. No. 6,511,809 B1, whereLHP-3 comprised a primary aliphatic amine group linked the 5′ terminus.

Ab1-SA-P1 and Ab2-P2, each with an Ab-probe conjugate concentration of 1nM, were mixed with 10 mM Tris-EDTA buffer and BSA and optionally 0.01-1nM IL-8. After 30 minutes at room temperature, the mixtures wereserially diluted so that the final concentration of Ab-probe conjugatewas in the fM range. The diluted mixtures were then mixed with SDAprimers SRH-1 and SLH-2, adapter ADR-5, and reporter probe TBD10.2.After the mixtures were warmed to 37° C. for 10 minutes, a portion ofeach sample was added to amplification wells at 52° C., as described inEXAMPLE 2, where each amplification reaction contained BsoBI restrictionenzyme and Bst DNA polymerase. The final concentration of the Ab-probeconjugates was 1 fM, and the final IL-8 concentration was 0, 0.01, 0.1or 1 fM. The concentrations of other components were as described inEXAMPLE 2. The samples were immediately transferred to a ProbeTec™ ETinstrument, where isothermal amplification was carried out for 1 hour at52° C. Amplification was monitored by observing the fluorescenceincrease as described in EXAMPLE 2.

Average MOTA values are reported in TABLE 5. Low MOTA values wereobtained for samples lacking IL-8, while higher levels of IL-8 resultedin increased MOTA values, confirming detection of IL-8 by the homogenousimmuno-SDA method. In this experiment, no hybridization blockeroligonucleotide was employed, but samples were diluted about amillion-fold after formation the proximity pair-IL-8 complex to reducethe occurrence of target-independent probe amplification.

TABLE 5 Detection of IL-8 by homogeneous immuno-SDA IL-8 concentrationAverage MOTA in binding mixture (pM) (n = 6) 0 492 10 3,983 100 73,8831,000 128,847

Example 8 Experimental Demonstration of Background Suppression by Use ofa Hybridization Blocker Oligonucleotide

This experiment illustrates the use of a hybridization blockeroligonucleotide to suppress target-independent amplification resultingfrom base-pairing between P1 and P2 molecules not associated with targetanalyte. In this experiment, probe P1 is 5′ biotinylated RHP-3, andprobe P2 is 5′ biotinylated LHP-3 (see above). The 10 nucleotidesequences comprising the 3′ ends of P1 and P2 are complementary to eachother. As in EXAMPLE 2, the target analyte is SA, which contains fourbiotin binding sites in its tetrameric form. The hybridization blockeroligonucleotide is RDB-3p8 (EXAMPLE 1), which comprises an 18-nucleotidesequence that is complementary to the 3′ end of RHP-3. A duplex formedbetween P1 and hybridization blocker RDB-3p8, therefore, will includethe 10 nucleotides at the 3′ end of P1 that are complementary to P2, aswell as an additional eight nucleotides of P1 that are not complementaryto P2. RDB-3p8 further comprises a 5′ tail sequence of 14 nucleotides(the bases 5′ of the underlined bases of RDP-3p8 in EXAMPLE 1), whichserve as a disabling template upon which the 3′ end of RHP-3 may beextended (depicted in FIG. 4C). A characteristic feature of thehybridization blockers of the present invention is that they do notbecome covalently attached or ligated to oligonucleotide moieties ofproximity members. In methods of the present invention that rely onextension of 3′ ends of oligonucleotide moieties to produceanalyte-specific amplicons, it is necessary for hybridizationblocker-probe duplexes to remain stable during polymerase-catalyzedamplification methods (such as SDA and PCR) that require extension of 3′ends and that typically occur at elevated temperatures where duplexesbecome less stable. The elevated temperatures typically employed inpolymerase-based amplification methods (e.g. PCR and SDA) can reduce theprevalence of probe-blocker hybrids to the point where suppression ofspurious probe conversion becomes ineffective. This difficulty isovercome in the present invention by selecting hybridization blockerscapable of forming probe-blocker hybrids that are more stable thanhybrids formed between probes, and by making use of the disablingtemplate, which stabilizes probe-blocker templates at elevatedtemperatures.

Analysis of SA-containing solutions by immuno-SDA was carried out asfollows. Solutions were prepared containing 20 pM each of 5′biotin-labeled probe RHP-3 (P1) and 5′ biotin-labeled LHP-3 (P2), 50 nMRDB-3p8 hybridization blocker oligonucleotide, 10 mM Tris-EDTA buffer,and 0.1 mg/ml BSA. Each solution also contained SA at 0, 0.1, 1, 10, or100 fM. The solutions were incubated for 2 hours at 37° C., and themixtures were diluted 10-fold in immuno-SDA buffer. 100 μL of thediluted samples were then mixed with 20 μL of a priming solutioncontaining 1.5 μM SRH-1 SDA primer, 3.75 μM SLH-2 SDA primer, 2.25 μMADR-8 adapter, 3.75 μM TBD10.2 reporter probe, and 0.375 μM RDB-3p8hybridization blocker oligonucleotide. The resulting mixtures wereincubated at 37° C. for 10 minutes. The sequences of alloligonucleotides may be found in EXAMPLE 1. To initiate an immuno-SDAreaction, 80 μL of each mixture were transferred to an amplificationmicrowell containing 20 μL of the SDA enzyme solution pre-equilibratedat 52° C. and comprised of Bst DNA polymerase, BsoBI restriction enzymeand other SDA components including potassium phosphate, BSA and dNTPs.The microwells then were sealed quickly, placed in a ProbeTec™ ETinstrument, and maintained at 52° C. for 1 hour as the fluorescence ofeach microwell was monitored. A series of control reactions that did notcontain the RDB-3p8 hybridization blocker oligonucleotide were prepared,along with those described above, and were monitored concurrently in theProbeTec™ ET instrument.

After accounting for dilution of the original binding mixtures, eachimmuno-SDA mixture contained 1.3 pM P1 and P2 and SA concentrations ofeither 0, 0.6, 6, 66, 666 or 6666 aM. The immuno-SDA reactions alsocontained 30 mM potassium phosphate (pH 7.6), 75 mM bicine, 50 mMpotassium hydroxide, 3.5% dimethylsulfoxide (DMSO), 5 mM magnesiumacetate, 50 μg/ml BSA, 500 nM SLH-2, 200 nM SRH-1, 50 nM RDB-3p8, 300 nMADR-8, 500 nM TBD10.2, 0.1 mM dATP, 0.1 mM dGTP, 0.1 mM dTTP, 0.5 mM2′-deoxycytidine 5′-O-(1-thiotriphosphate) S-isomer (dCTPαS),approximately 8 units of Bst DNA polymerase and 18 units of BsoBIrestriction enzyme. Amplification of products resulting from mutualhybridization and extension of P1 and P2 (see FIG. 1) were detected bymonitoring the increase in ROX fluorescence associated withamplification of the TBD10.2 reporter oligonucleotide through theadapter-mediated process described in U.S. Pat. No. 6,316,200. For eachwell, one ROX reading was made every minute during the course of thereaction. The ROX fluorescence readings for each sample were plottedover a time period of 60 minutes.

MOTA values are reported in TABLE 6. For target-free reactions (i.e., 0aM SA) without the hybridization blocker oligonucleotide, a relativelyhigh average MOTA value of 49,382 was obtained. This background signalsignificantly limits the sensitivity of immuno-amplification and isbelieved to arise from target-independent hybridization of P1 with P2and subsequent extension of their 3′ ends, which converts the probesinto amplifiable products even in the absence of target analyte.Background signal is dramatically reduced, however, when a hybridizationblocker oligonucleotide is included in the reaction mixtures, asrevealed by the low average MOTA value of 376 obtained from thetarget-free mixtures with RDB-3p8. In these reactions, the hybridizationblocker oligonucleotide binds competitively to the 3′ end of P1, therebypreventing P2 from hybridizing to P1 and essentially eliminatingtarget-independent conversion of the probes into amplifiable products.

Reaction mixtures containing both the target analyte SA and the RDB-3p8hybridization blocker oligo-nucleotide exhibit high MOTA values,indicating efficient amplification of target bound probes even in thepresence of the hybridization blocker oligonucleotide. The inventorsestimate that concurrent binding of probes P1 and P2 to the samemolecule of SA increases the local concentration of the two probes byover 10 million-fold relative to unbound probes in bulk solution. Theestimated effective local concentration of the two probes on the SAmolecule is greater than 10 μM, which greatly exceeds the 50 nMconcentration of hybridization blocker oligonucleotide in bulk solution.The high local concentration of target-bound P1 and P2 promotes mutualhybridization of the probes and conversion of the probes intoamplifiable products, despite the presence of the competinghybridization blocker oligonucleotide. By contrast, probes P1 and P2 notbound to target have a concentration in bulk solution of 1.3 pM, andmutual hybridization of these unbound probes is efficiently suppressedby competitive hybridization of the hybridization blockeroligonucleotide with P1. While some suppression of target-bound probeconversion appears to occur, as revealed by reduced MOTA scores for theSDA reactions at 666 aM SA containing the hybridization blocker comparedwith reactions at 666 aM SA without the blocker, the ratio of targetsignal/background signal is nearly 200-fold greater for reactionscontaining the hybridization blocker.

TABLE 6 MOTA values from SDA-based detection of SA with or without ahybridization blocker oligonucleotide MOTA with 50 nM SA concentrationhybridization in SDA reaction blocker oligo- MOTA without (aM)nucleotide RDB-3p8 RDB-3p8 0 376 49,382 0.6 1,037 N.D. 6 6,075 N.D. 6638,815 N.D. 666 73,175 109,142  6666 98,790 N.D.

In general, reaction mixtures containing higher concentrations ofunbound probes P1 and P2 will require increased concentrations ofhybridization blocker oligonucleotide to provide the same degree ofbackground suppression as samples containing lower probe concentrations.The concentration of hybridization blocker oligonucleotide may beadjusted empirically to determine the concentration needed to provide anadequate degree of background suppression. Because high concentrationsof hybridization blocker oligonucleotide also may suppress amplificationof target-bound probes to some degree, the lowest concentration of ahybridization blocker oligonucleotide found to give adequate backgroundsuppression will generally be optimal.

The hybridization blocker oligonucleotide employed in this example,RDB-3p8, contains an 18-nucleotide sequence that is complementary to the3′ end of probe P1, RHP-3, such that hybridization of RDB-3p8 to RHP-3creates an 18-base pair duplex and unpaired, single-stranded tails onthe 5′ ends of each oligonucleotide. Hybridization blockeroligonucleotides having a complementary sequence either longer orshorter than RDB-3p8 (e.g., RDB-3p10 or RDB-3p5, respectively) also maybe employed. In general, for a given concentration, hybridizationblocker oligonucleotides with shorter segments of probe complementaritywill form duplexes with P1 that are of lower stability (lower T_(m))than those with longer segments of probe complementarity. Hybridizationblocker oligonucleotides that form less stable duplexes with a givenprobe generally will need to be employed at higher concentrations toprovide the same degree of background suppression as hybridizationblocker oligonucleotides that form more stable duplexes with the probe.The stability of the P1:P2 duplex also will affect the efficiency of agiven hybridization blocker oligonucleotide. In general, the more stablethe P1:P2 duplex, the higher the concentration of a given hybridizationblocker oligonucleotide that must be employed to impart a suitable levelof background suppression. Likewise, the more stable the P1:P2 duplex,the more stable the probe-blocker duplex must be to impart the samedegree of background suppression for a fixed concentration ofhybridization blocker oligonucleotide. The stability of the duplexformed between a hybridization blocker oligonucleotide and probe can bemodulated by changing the length or sequence composition of thehybridization blocker oligonucleotide sequence that is complementary tothe probe. Software for estimating the duplex stability from parameterssuch as oligonucleotide sequence and concentration are well-known in theart, such as OLIGO® (Cambio, United Kingdom) and Mfold (copyright 1996Dr. M. Zuker) (see http://www.bioinfo.rpi.edu/applications/mfold,described in Zuker, Nucl. Acids. Res. 31:3406-15 (2003), incorporatedherein by reference).

Two hybridization blocker oligonucleotides, one specific for each probe,may be employed simultaneously to suppress background signal. Ingeneral, lower concentrations of hybridization blocker oligonucleotidesare required to impart the same degree of background suppressionobtained with a single hybridization blocker oligonucleotide.

Example 9 Homogeneous Detection of Sub-Picomolar IL-8 Concentrations byImmuno-SDA

Antibody-probe conjugates Ab1-SA-P1 and Ab2-P2 were as described inEXAMPLE 7. 50 μL samples containing 10 mM Tris-EDTA buffer, 20 pMAb1-SA-P1, 100 pM Ab2-P2, 1 mg/mL BSA, 0.1 mg/mL mouse gamma globulin,50 nM hybridization blocker oligonucleotide RDB-3z8, and IL-8 at 0,0.005, 0.010, or 0.025 μM were prepared. After incubating for 3 hours atroom temperature, an 5 μL aliquot of each sample was diluted 1:10 (v/v)into Tris-EDTA buffer containing 0.1 mg/mL BSA and then further diluted1:10 (v/v) into a 100 μL solution containing SDA primers SRH-1 (100 nM)and SLH-2 (500 nM), 300 nM adapter primer ADR-8, 500 nM reporter probeTBD10.2(D/R), and 50 nM hybridization blocker RDB-3z8. Four such dilutedmixtures were prepared from each original sample. The diluted mixtureswere then incubated at 37° C. for approximately 10 minutes before an 80μL aliquot of each mixture was transferred into a separate microwellcontaining 20 μL of SDA enzyme solution that had been pre-warmed to 52°C. The microwells were sealed, placed into a ProbeTec™ ET instrument andincubated at 52° C. for 1 hour. Amplification was monitored by observingthe fluorescence increase associated with conversion of thefluorescein-labeled reporter probe, TBD10.2, as described in U.S. Pat.No. 6,316,200, herein incorporated by reference. Resulting MOTA valuesare reported in TABLE 7. Average MOTA values for binding mixturescontaining IL-8 concentrations as low as 0.005 pM are significantlyhigher than the values from the zero IL-8 samples, confirming theability of the current homogeneous method to detect analyteconcentrations in the low femtomolar range without separating bound fromunbound antibodies.

Background signals, represented by MOTA scores in the zero IL-8 samples,are thought to result from spurious amplicon formation arising throughweak interactions between antibodies not bound to target (see EXAMPLE16). Background levels are higher in this example than in EXAMPLE 7because antibody concentrations in SDA reactions of the current examplewere at least 200-fold higher than in the earlier example.

TABLE 7 Homogeneous detection of sub-picomolar IL-8 concentrations byimmuno-SDA [IL-8] in Average MOTA (n = 4) binding mix standard error0.000 pM 12,800 ± 3,800 0.005 pM 27,300 ± 4,300 0.010 pM  47,600 ±12,000 0.025 pM 96,500 ± 2,900

Example 10 Experimental Demonstration of Immuno-SDA Employing a TetherOligonucleotide and a Bridging Probe to Detect IL-8

10 nM of the Ab1-SA conjugate of EXAMPLE 9 was mixed with 20 nM3′-biotin labeled RCP-1 tether oligonucleotide (TO) in 0.1 M Tris-EDTAbuffer containing 0.1 mg/mL BSA. This mixture was incubated overnight at4° C. to permit the biotinylated oligonucleotide to bind the Ab1-SAconjugate, forming Ab1-SA-TO.

Mixtures containing 1 nM Ab1-SA-TO, 1 nM RHP-3 with no biotin label(P1), 1 nM Ab2-P2 (see EXAMPLE 8), 10 mM Tris-EDTA buffer, 0.1 mg/mLBSA, and IL-8 at 0, 10 or 100 pM were prepared. After incubating for 30minutes at room temperature, the mixtures were serially diluted so thatthe final concentration of Ab-probe conjugates was in the fM range. Thediluted mixtures then were mixed with SDA primers SRH-1 and SLH-2,adapter ADR-5, and reporter probe TBD10.2, and the mixtures were warmedto 37° C. for 10 minutes. A portion of each diluted sample was added todried amplification wells at 52° C. as described in EXAMPLE 2, whichalso contained the BsoBI restriction enzyme and Bst DNA polymerase. Theconcentrations of Ab-probe conjugates in resulting SDA mixture were 1fM, and the IL-8 concentration was either 0, 0.01, or 0.1 fM. Thesamples were immediately transferred to a ProbeTec™ ET instrument, whereisothermal amplification was carried out for 1 hour at 52° C.Amplification was monitored by observing the fluorescence increase asdescribed in EXAMPLE 2 above.

MOTA values are reported in TABLE 8. Low MOTA values were obtained forsamples lacking IL-8, while higher levels of IL-8 resulted in increasedMOTA values, confirming detection of IL-8 by an immuno-SDA method inwhich P1 is employed as a splint oligonucleotide linked indirectly toanalyte binding moiety Ab1 through hybridization with a tetheroligonucleotide TO, as depicted in FIG. 3A. In this experiment, nohybridization blocker oligonucleotide was employed, and samples werediluted about a million-fold after formation the proximity pair-IL-8complex to reduce the occurrence of target-independent probeamplification.

TABLE 8 Detection of IL-8 by homogeneous immuno- SDA with tetheroligonucleotide IL-8 concentration Average MOTA in binding mixture (pM)(n = 6) 0 345 10 505 100 32,227

Example 11 Experimental Demonstration of Immuno-SDA Employing a Fab′Fragment as Analyte Binding Moiety in the Detection of IL-8

MAb G265-8 (see EXAMPLE 9) was digested with pepsin to yield F(ab′)₂fragments and fragments of the Fc region. F(ab′)₂ was purified andfurther treated with dithiothreitol (DTT) to reduce the disulfidebridges linking the Fab′ fragments. The resulting Fab′ fragment (Ab1)was coupled to two RHP-3 oligonucleotides (P1) to form an Ab1-P1conjugate.

Mixtures containing 0.1 nM Ab1-P1, 0.1 nM Ab2-P2 (see EXAMPLE 8), 10 mMTris-EDTA buffer, 0.1 mg/mL BSA, 10 nM hybridization blockeroligonucleotide RDB-3p8 (see EXAMPLE 1), and IL-8 at 0, 0.1 or 1 pM wereprepared. After incubating 3 hours at 37° C., the mixtures were seriallydiluted so that the resulting concentration of Ab-probe conjugates wasin the fM range. The diluted mixtures were then mixed with SDA primersSRH-1 and SLH-2, adapter ADR-5, additional hybridization blocker RDB-3p8to a final concentration of 10 nM, and reporter probe TBD10.2. Theresulting mixtures were maintained at 37° C. for 10 minutes. A portionof each sample was then added to dried amplification wells at 52° C. asdescribed in EXAMPLE 2, which also contained the BsoBI restrictionenzyme and Bst DNA polymerase. In the resulting SDA mixtures, theconcentrations of the Ab-probe conjugates were 100 fM and the IL-8concentration was either 0, 0.1 or 1 fM (TABLE 9). The samples wereimmediately transferred to a ProbeTec™ ET instrument, where isothermalamplification was carried out for 1 hour at 52° C. Amplification wasmonitored by observing the fluorescence increase, as described inEXAMPLE 2.

TABLE 9 Detection of IL-8 by homogeneous immuno-SDA with Fab′-P1conjugate IL-8 concentration Average MOTA in binding mixture (pM) (n =6) 0 1,920 0.1 4,713 1 19,710

Average MOTA values for four replicates are reported in TABLE 9. LowMOTA values were obtained for samples lacking IL-8, while higher levelsof IL-8 resulted in increased MOTA values, confirming detection of IL-8by the immuno-SDA method in which a Fab′ is employed as the analytebinding moiety of Ab1-P1.

Example 12 Target-Mediated Amplicon Formation Using ReversiblyImmobilized Proximity Member, Combined with Background Suppression Usinga Hybridization Blocker Oligonucleotide

The buffers used in this example are as follows:

-   -   TBS: 25 mM Tris (pH 7.6), 150 mM NaCl;    -   Diluent A: Diluent B plus 0.01% Tween-20, 800 μM D-biotin and 5        mM EDTA;    -   Diluent B: TBS, 0.5% Skim Milk Powder (Oxoid Ltd., United        Kingdom), 0.1 mg/mL molecular biology grade DNA (Roche Molecular        Systems, Pleasanton, Calif.);    -   Blocking Solution: TBS, 4.5% Skim Milk Powder, 1 mg/mL molecular        biology grade DNA, 2 mg/mL sodium azide, 5 mM EDTA;    -   Wash Buffer: TBS, 5 mM EDTA, 0.05% Tween-20;    -   SDA Reaction Buffer (Concentrated): 90 mM bicine, 60 mM KOH, 12        mM potassium phosphate, 6.57% glycerol, 4.23% DMSO;    -   SDA Primer Mix: 7.5 μM SRH-1, 37.5 μM SLH-2, 300 μM ADR-5, 37.5        μM TBD10.2 in water; and    -   SDA Enzyme Mix: 18 units BsoBI restriction endonuclease and 8        units Bst polymerase (BD Diagnostic Systems) in 75 mM Bicine, 50        mM potassium hydroxide, 10 mM potassium phosphate (pH 7.6).

The chosen target analyte is IL-8, and MAbs G265-5 and G265-8 are theanalyte-binding moieties. MAb G265-5 was conjugated to probe LHP-3 toproduce Ab1-P1. MAb G265-8 was conjugated with SA, and this conjugatewas mixed with the 5′ biotinylated probe RHP-3 at a ratio of two probesper Ab molecule to produce Ab2-P2.

A capture oligonucleotide was immobilized to a solid support accordingto the following procedure. SA-coated 96-microwell plates (Pierce Cat.No. 15121) were rinsed three times in TBS and incubated overnight inBlocking Solution before being washed four times with Wash Buffer. A 100μL solution containing 80 nM of 5′-biotinylated RCP-9v2.2 captureoligonucleotide was added to each well and incubated for 1 hour at roomtemperature. The plates were then washed four times with Wash Buffercontaining 800 μM D-biotin.

Hybridization of the Ab2-P2 conjugate to the immobilized captureoligonucleotide was performed as follows: 100 μL of 0.1 nM Ab2-P2 inDiluent A was added to each microwell and incubated at room temperaturefor 1 hour. The microwells were then washed four times with Wash Buffer.100 μL of a sample solution containing either 0 or 50 pM IL-8 in DiluentB was then added to each microwell and incubated at room temperature for1 hour. The microwells were then washed four times with Wash Buffer.This step resulted in a complex formed between IL-8 and the immobilizedAb2-P2.

Binding of Ab1-P1 to the complex between IL-8 and the immobilized Ab2-P2was performed as follows: a 100 μL solution of 0.1 nM Ab1-P1 conjugatein Diluent A, containing either 1 μM LBK-1 hybridization blockeroligonucleotide or no hybridization blocker oligonucleotide, was addedto the microwells containing the complex between IL-8 and Ab2-P2 andincubated at room temperature for 1 hour. Microwells containing theLBK-1 hybridization blocker oligonucleotide were then washed five timesin Wash Buffer containing 1 μM LBK-1, followed by two washes with WashBuffer devoid of LBK-1. Microwells not exposed to the hybridizationblocker oligonucleotide were washed seven times with Wash Buffer. Forboth sets of wells, two final washes were carried out with TBS.

The captured complexes prepared as described above were eluted from thesupport by addition of 120 μL of SDA Reaction Buffer (Concentrated) andincubated at room temperature for 20 minutes. A 100 μL volume containingthe eluted complexes was transferred from each microwell to a newmicrowell containing 20 μL of the SDA Primer Mix. The microwells wereincubated for 20 minutes at room temperature and then placed on a 37° C.heat block for 10 minutes. To initiate amplification by SDA, 80 μL wasremoved from each 37° C. microwell and transferred to a separatemicrowell containing 20 μL of SDA Enzyme Mix that had been pre-heated to52° C. The microwells then were quickly placed into a BD ProbeTec™ ETinstrument and maintained at 52° C. for 1 hour while fluorescenceintensity was monitored during the course of amplification. The MOTAvalue for each amplification reaction was determined from the kineticfluorescence profile obtained during the course of the reaction.

As depicted in FIG. 7D, base-pairing between the probe moieties P1 andP2 of antibody-probe conjugates Ab1-P1 and Ab2-P2 promotes formation oftarget-free binary complexes between the two antibody-probe conjugates.Inclusion of hybridization blocker oligonucleotide LBK-1 in bindingmixtures suppresses formation of the target-free complexes by precludingbase-pairing between P1 and P2. The presence of target-free binarycomplexes in the absence of the hybridization blocker oligonucleotideresulted in high levels of background signal during immuno-amplificationreactions, as revealed in TABLE 10 by the high average MOTA valueassociated with binding mixtures that contained no IL-8 and no LBK-1hybridization blocker oligonucleotide. By contrast, the presence of 1 μmLBK-1 hybridization blocker oligonucleotide reduces the average MOTAvalue for the “no IL-8” binding mixtures by 20-fold, indicatingsubstantial reduction in the formation of the target-free complexes. Thepresence of the hybridization blocker oligonucleotide reduces theintensity of the IL-8 specific signal slightly (compare MOTA values ofthe 50 pM IL-8 mixtures with and without LBK-1); however, the ratio ofspecific signal to background signal is 12-fold higher for bindingmixtures that contained the hybridization blocker oligonucleotide thanfor those that did not.

The results further demonstrate the use of an immobilized proximitymember (Ab2-P2) to capture or immobilize a target antigen (IL-8) and toform an immobilized ternary complex comprising the target antigen andboth members of a proximity pair (Ab1-P1 and Ab2-P2), as depicted inFIGS. 7A-7G. This example also reveals that a detectable number of theimmobilized ternary complexes become detached from the solid-phaseduring the 20-minute room temperature elution period following additionof the concentrated SDA buffer, even though the estimated half-life ofthe immobilizing hybrid (the duplex formed between captureoligonucleotide and probe moiety P2) is much longer (many days) than the20-minute elution time.

TABLE 10 Average MOTA values (n = 6) from immuno-SDA detection of IL-8using immobilize proximity member with or without a hybridizationblocker oligonucleotide With 1 μM Without LBK- 1 hybrid- hybridizationIL-8 concentration ization blocker blocker in Binding Mixture (pM)oligonucleotide oligonucleotide 0 1,533 31,829 50 66,404 112,451

Example 13 Target-Mediated Amplicon Formation Using ReversiblyImmobilized Proximity Member: Release of Immobilized Complex byApplication of Low-Ionic Strength Solution

The MAbs, analyte and buffers used in this example are the same as thosedescribed in EXAMPLE 12. Biotinylated RCP-9v2.2 capture oligonucleotidewas immobilized on a support in the same manner as described in EXAMPLE12. Hybridization of the Ab2-P2 conjugate to the immobilized captureoligonucleotide was performed as described in EXAMPLE 12. 100 μL DiluentB containing either 0 or 10 pM IL-8 then was added to each microwell,which were incubated at room temperature for 1 hour. The microwells thenwere washed four times with Wash Buffer. Diluent A containing 0.1 nM ofthe Ab1-P1 conjugate and 1 μM of the LBK-1 hybridization blockeroligonucleotide was then added to each microwell, and the microwellswere incubated at room temperature for 1 hour. Microwells then werewashed as described in EXAMPLE 12, except that the final two wash stepscontained 10 mM NaCl rather than TBS.

To release the resulting immobilized complex between IL-8 and the Ab1-P1and Ab2-P2 conjugates, each microwell was treated with either 75 μLwater or non-concentrated SDA Buffer. After incubating for 20 minutes atroom temperature, 70 μL of this solution was removed and analyzed by SDAas described in EXAMPLE 12.

This example demonstrates the use of a low-ionic strength solution torelease intact the immobilized ternary complex comprised of an IL-8molecule bound simultaneously to the proximity pairs Ab1-P1 and Ab2-P2.The results of this example are shown in TABLE 11. The average MOTAvalue obtained for samples containing 10 pM IL-8 that were eluted withwater (low ionic strength) is nearly 10-fold higher than the averageMOTA value for samples eluted with SDA buffer (moderate ionic strength),confirming the release of the ternary complex by application of alow-ionic strength solution as depicted in FIG. 7I.

TABLE 11 Average MOTA values (n = 6) from immuno-SDA detection of IL-8using an immobilized proximity member: Elution at low ionic strength orat moderate ionic strength Elution with Elution with SDA buffer IL-8concentration water (low (moderate in Binding Mixture (pM) ionicstrength) ionic strength) 0 148 220 10 46,584 4,888

Example 14 Target-Mediated Amplicon Formation Using ReversiblyImmobilized Proximity Member: Release of Immobilized Complex byApplication of a Displacement Oligonucleotide

The MAbs, analyte and buffers are the same as those described in EXAMPLE12. Biotinylated RCP-9v2.2 capture oligonucleotide was immobilized on asupport in the same manner as described in EXAMPLE 12. Hybridization ofthe Ab2-P2 conjugate to the immobilized capture oligonucleotide wasperformed as described in EXAMPLE 12. 100 μL Diluent B containing either0 or 10 pM IL-8 then was added to each microwell, which were incubatedat room temperature for 1 hour. The microwells then were washed fourtimes with Wash Buffer. Diluent A containing 0.1 nM of the Ab1-P1conjugate and 1 μM of the LBK-1 hybridization blocker oligonucleotidewas then added to each microwell, and the microwells are incubated atroom temperature for 1 hour. Microwells then were washed as described inEXAMPLE 12.

To release the resulting immobilized complexes between IL-8 and theAb1-P1 and Ab2-P2 conjugates, each microwell was treated with 120 μL ofSDA Buffer (Concentrated) that either contained 0.1 μM of the CMPR-9v2displacement oligonucleotide or no displacement oligonucleotide. Afterincubating for 20 minutes at room temperature, this solution wasanalyzed by SDA as described in EXAMPLE 12.

This example demonstrates the use of a displacement oligonucleotide torelease intact the immobilized ternary complex comprised of an IL-8molecule bound simultaneously to proximity pairs Ab1-P1 and Ab2-P2. Theresults of the current example are shown in TABLE 12. The average MOTAvalue obtained for samples containing 10 pM IL-8 and treated with thedisplacement oligonucleotide is 10-fold higher than the MOTA value for10 pM IL-8 samples not treated with the displacement oligonucleotide,confirming the release mechanism depicted in FIG. 7J.

TABLE 12 Average MOTA values (n = 6) from immuno-SDA detection of IL-8using an immobilized proximity member with or without a displacementoligonucleotide With 0.1 μM CMPR-9v2 Without IL-8 concentrationdisplacement displacement in Binding Mixture (pM) oligonucleotideoligonucleotide  0 pM 97 220 10 pM 54,702 4,888

Example 15 Experimental Demonstration of Immuno-SDA Using a 3′-CappedProximity Probe

This example provides an experimental demonstration of the processdepicted in FIG. 14, namely the use of a 3′-capped, non-extendibleproximity probe for detection of an analyte by immuno-amplification. Thetarget analyte in this example is SA. The 3′-capped proximity probe P1is LHP-3 [cap] (shown in EXAMPLE 1). LHP-3 [cap] comprises a 3′dexoyuridine moiety that prevents extension of the probe when LHP-3[cap] is hybridized to the complementary template strand P2. In thisexample, the analyte binding moiety is a biotin moiety attached to the5′ end of LHP-3 [cap]. The second probe of the proximity pair, P2, isRHP-3 (shown in EXAMPLE 1), which comprises a 5′ biotin moiety and anextendible 3′ end. An uncapped control probe, LHP-3, comprises a 5′biotin moiety and an extendible 3′ end. Amplification primers, adapteroligonucleotide, reporter probe, hybridization blocker oligonucleotideand other reaction components are the same as EXAMPLE 8.

Solutions were prepared containing 20 pM 5′ biotin RHP-3, 20 pM 5′biotin LHP-3 [cap], 10 mM Tris-EDTA buffer, 5 μg/mL BSA, and either 0 or10 fM SA. The binding mixtures optionally contained 100 nM RDB-3p5hybridization blocker oligonucleotide (see TABLE 13). The bindingmixtures were incubated at 37° C. for 2 hours and then diluted 10-foldand subjected to SDA as described in EXAMPLE 8. A control mixture, inwhich LHP-3 [cap] was replaced by uncapped LHP-3, was also prepared andsubjected to SDA as described above. Average MOTA values from thevarious SDA reactions are shown in TABLE 13.

TABLE 13 Average MOTA values (n = 4) from immuno-SDA detection of SAusing 3′-capped or uncapped P1 probe Concentration of RDB-3p5hybridization blocker oligonucleotide SA concentration 0 100 nM 0 100 nMin Binding Mix (fM) P1 = LPH-3 [cap] P1 = LPH-3 (no cap) 0 36,355 2,98555,588 4,683 10 N/D 133,325 N/D 115,143

As indicated by MOTA values for samples without SA, reactions in whichthe proximity probe P1 contained a 3′-extension cap (LHP-3 [cap])exhibited significantly lower background signal than reactionscontaining the uncapped probe (LHP-3). For both capped and uncappedprobes, the presence of a hybridization blocker oligonucleotidesuppressed background signal by about 12-fold relative to the samereaction mixtures devoid of the hybridization blocker oligonucleotide.While the background signal was lower with the capped probe, signal inthe presence of 10 fM SA was slightly higher for the capped probe versusthe uncapped probe, indicating efficient conversion of the capped P1 anduncapped P2 probes into amplifiable products in the presence of thetarget analyte. This example further demonstrates that analyte-specificamplicon formation can occur when only one of the overlapping 3′ endsformed by a probe-probe hybrid comprises a 3′ OH group.

Example 16 Experiment Revealing Antibody-Antibody Interactions as aSource of Target-Independent Amplicon Formation

This example demonstrates that the interaction between the Ab moietiesof the proximity members contributes to target-independentamplification. Four test solutions were prepared containing thecomponents listed below, as described in EXAMPLE 9, in a solution of 10mM Tris-EDTA buffer and 0.1 mg/mL BSA:

-   -   Test Solution 1: 1 nM Ab1-P1 and 1 nM Ab2-SA-P2;    -   Test Solution 2: 1 nM Ab1-P1, 1 nM unconjugated Ab2 and 2 nM        unconjugated P2;    -   Test Solution 3: 1 nM unconjugated Ab1, 2 nM unconjugated P1 and        1 nM Ab2-P2; and    -   Test Solution 4: 2 nM unconjugated-P1 and 2 nM unconjugated P2.

The test solutions were incubated for 30 minutes at 37° C. and thenserially diluted so that the resulting concentrations of antibodies,probes and conjugates were in the pM range. The diluted mixtures werethen mixed with SDA primers and enzymes and subjected to SDA asdescribed in EXAMPLE 9, except that the SDA reaction mixtures optionallycontained 50 nM RDB-3p8 hybridization blocker oligonucleotide. Further,the unconjugated probes were used at twice the molar ratio ofantibody-probe conjugates to reflect the known probe:antibody ratio of2:1 in the conjugates. No target analyte was present in the reactions,so MOTA values produced are attributable solely to target-independentprobe conversion.

The average MOTA values from the various test solutions are reported inTABLE 14. In reaction mixtures without hybridization blockeroligonucleotides, average MOTA values exceeded 100,000 for all testsolutions. In Test Solution 4, containing 50 nM RDB-3p8 hybridizationblocker oligonucleotide, average MOTA values were reduced to below20,000, indicating a greater than 5-fold suppression of backgroundsignal. By contrast, the MOTA values for Test Solution 1 were reducedonly about 2-fold to ˜59,000 by the presence of the hybridizationblocker oligonucleotide, indicating that blocking efficiency provided byRDB-3p8 is lower in the presence of two intact antibody probe conjugatesthan in the presence of the unconjugated probes P1 and P2. The higherMOTA values of Test Solution 1 compared with Test Solution 4 implies theoccurrence of antibody-mediated amplicon formation in Test Solution 1and further suggests that target-independent adherence of Ab1 and Ab2 toeach other brings the attached probe moieties into sufficiently closeproximity to facilitate spurious amplicon formation. Apparently, becausethe local probe concentration in mutually adhering antibody pairs ismuch higher than the overall probe concentration in bulk solution,hybridization blocker oligonucleotides cannot suppresstarget-independent probe conversion in Test Solution 1 as effectively asin Test Solution 4, where adhering antibody pairs cannot form. This isconsistent with the results of Test Solutions 2 and 3, which exhibitMOTA values comparable to those of Test Solution 4, indicating that bothprobe moieties of a proximity pair must be antibody-conjugated toproduce the high MOTA values attributed to the antibody-mediated probeconversion seen in Test Solution 1.

TABLE 14 Background signal (average MOTA values, where n = 6) producedby various combinations of proximity components With 50 nM RDB-3p8Without hybridization hybridization Test Proximity blocker blockerSolution components oligonucleotide oligonucleotide 1 Ab1-P1 + Ab2-P259,309 133,521 2 Ab1-P1 + Ab2 + P2 14,444 110,704 3 Ab1 + P1 + Ab2-P217,185 121,298 4 P1 + P2 19,674 103,114

Example 17 Detection of IL-8 by Immuno-SDA Employing a Probe withReversed Opposite Sequence Orientation

This example provides an experimental demonstration of the conceptdepicted in FIG. 1J. Antibody conjugates Ab1-SA and Ab2-P2 were asdescribed in EXAMPLE 7. Ab1-SA was incubated overnight at 4° C. withprobe RBD-3v3 at a probe:antibody ratio of 2:1 to form Ab1-SA-P1. Asnoted in EXAMPLE 1, RBD-3v3 contains a biotin-moiety near its 3′terminus. Samples containing 10 mM Tris-EDTA buffer, 20 pM Ab1-SA-P1,100 pM Ab2-P2, 1 mg/mL BSA, 50 nM hybridization blocker oligonucleotideRDB-3z8, and IL-8 at 0, 0.1, 0.25, 0.5 and 1.0 μM were prepared. Afterincubating for 3 hours at room temperature, an aliquot of each standardsample was diluted 1:10 (v/v) into Tris-EDTA buffer containing 0.1 mg/mLBSA and further diluted 1:10 (v/v) into a solution containing SDAprimers (SRH-1 and SLH-2), adapter primer (adr-8), reporter probe(TBD10.2(D/R)), and 50 nM hybridization blocker (RDB-3z8). In the SDAreactions, primer, adapter and reporter concentrations were as describedin EXAMPLE 18, and hybridization blocker RDB-3z8 concentration was 50nM. Four replicates of these diluted mixtures were prepared from eachoriginal sample. The diluted mixtures were then incubated at 37° C. forapproximately 10 minutes before an 80 μL aliquot of each mixture wastransferred into a separate microwell containing 20 μL of SDA enzymesolution that had been pre-warmed to 52° C. The microwells were sealed,placed into a ProbeTec™ ET instrument and incubated at 52° C. for 1hour. Amplification was monitored by observing the fluorescence increaseas described in EXAMPLE 9.

Average MOTA values are reported in TABLE 15. Low MOTA values wereobtained for samples lacking IL-8, while increasing levels of IL-8resulted in progressively higher MOTA values, confirming detection ofIL-8 by an immuno-SDA method in which one of the probes is joined to anantibody through a linkage near its 3′ end as depicted in FIG. 1J. Theresults further confirm that a probe-probe (P1-P2) duplex comprisingonly one extendible 3′ OH group can produce an analyte-specificamplicon.

TABLE 15 Detection of IL-8 by homogeneous immuno- SDA with reversedprobe (rbd-3v3) IL-8 concentration Average MOTA in binding mixture (pM)(n = 4) 0 3,069 0.1 23,098 0.25 81,641 0.5 118,338 1.0 128,724

Example 18 Quantification of IL-8 by Immuno-SDA Employing an InternalNucleic Acid Control and Proximity Pair

This example illustrates absolute quantification of a target analyte (inthis case IL-8) in a test sample using the ratio of two fluorescencesignals resulting from co-amplification of a nucleic acid control and atarget amplicon produced from analyte-bound proximity members,respectively. According to the present invention, a plurality ofstandard samples and at least one test sample are initially formed. Theplurality of standard samples each contain a known starting quantity ofa nucleic acid control sequence, a known starting quantity of targetanalyte, and a quantity of proximity pairs of the invention. Typically,different members of the plurality of the standard samples will havedifferent known quantities of target analyte. The test sample contains aknown starting quantity of the nucleic acid control sequence, an unknownquantity of a non-nucleic acid target analyte, and a quantity of theproximity pair. It is this unknown quantity of the target analyte thatis to be determined by the absolute quantification method.

In standard and test samples, the oligonucleotide moieties of proximitymembers that are bound concurrently to the same target analyte moleculeare converted into amplicons by any of the methods of the inventiondescribed above. The resulting amplicons and nucleic acid controlsequences in each standard and test sample are then co-amplified. Withineach sample, amplification of amplicons and control sequences mayproduce separately detectable fluorescence emissions, so that theamplification of the amplicons and control nucleic acid within the samesample may be monitored independently at different fluorescence emissionwavelengths during the course of amplification.

The fluorescence values obtained during amplification may be displayedas a two-dimensional graph, termed a “real-time fluorescence profile,”with measurement time points assigned to the abscissa and thefluorescence values assigned to the ordinate. FIG. 15A shows an exampleof a two-color, real-time fluorescence profile of a sample resultingfrom co-amplification of target and control amplicons in the experimentsdescribed below. The detection wavelengths used in the current examplewere those characteristic for the fluorescent dyes rhodamine andfluorescein, which were used to label the reporter oligonucleotides thatare specific for the target amplicon and control nucleic acid,respectively.

For each of the standard and test samples, fluorescence intensities weremeasured at the two independent detection wavelengths over a plurality nof time-points, which comprise the amplification interval. For a givensample i, each time-point (tp) has two associated fluorescence values,one corresponding to amplified target amplicon (FT(tp)_(i)) and theother to amplified control nucleic acid (FC(tp)_(i)). These tworeadings, gathered from the same sample at the same time interval, arereferred to as a “matched pair” of fluorescence values.

For purposes of analysis, real-time fluorescence profiles of two or moredifferent samples are assumed to be temporally coherent; that is, thesame time-point from two or more different samples corresponds to thesame measure of elapsed time following initiation of amplification inthe respective samples. These equivalent time-points from differentsamples are said to be “coincident.” In the event that raw fluorescenceprofiles of different samples are not temporally coherent, methods knownin the art may be employed to construct temporally coherent “normalized”profiles from the raw data (see, e.g., U.S. Pat. No. 5,863,736 and No.6,066,458, the disclosures of which are incorporated herein by referencein their entirety).

For each time-point (tp) within the real-time fluorescence profile of agiven sample i, each matched pair of fluorescence values may be used tocompute a signal ratio, SR(tp)_(i) according to the relationship(Equation 1):

SR(tp)_(i) =[FT(tp)_(i) −FT(base)_(i) ]/[FC(tp)_(i)−FC(base)_(i)]  Equation 1,

in which the baseline fluorescence measurements, FT(base)_(i) andFC(base)_(i), correspond to the respective fluorescence intensitiesprior to detectable amplification of target and control amplicons. Inpractice, FT(base)_(i) is taken as the average value of the targetamplicon fluorescence measured over the first several time-points duringamplification of sample i, and FC(base)_(i) is taken as the averagenucleic acid control fluorescence measured over those same time-points,although other approximations of baseline fluorescence may also beemployed.

Each pair of real-time target and control fluorescence profilesresulting from an amplified sample will, therefore, give rise to nsignal ratios, where n is the number of time-points in the profile.Likewise, each time-point that is coincident across a plurality of ksamples will have k “coincident” signal ratios, SR(tp)_(i), associatedwith it, where each signal ratio corresponds to a sample i at thecoincident time-point tp.

To correlate between the signal ratios produced by a sample and thequantity of analyte (IL-8) contained in the sample, signal ratiosdetermined for a plurality of k standard samples containing variousknown quantities of IL-8 were analyzed as follows. Each set ofcoincident signal ratios (i.e., signal ratios derived from the sametime-point, tp, across all k standard samples) was first subjected tolinear regression against the known analyte concentrations according toEquation 2, which defines a “calibration” line relating the quantitieslog(SR(tp)_(i)) and log([IL-8]_(i)) and possessing slope, m(tp), andintercept, b(tp), values determined by the regression routine:

log(SR(tp)_(i))={m(tp)log([IL-8]_(i))}+b(tp)  Equation 2.

This operation is repeated for each of the n sets of coincident signalratios, producing n calibration lines defined by n pairs of slope andintercept values, each pair corresponding to a different coincidenttime-point across the plurality of k standard samples. One of the ncalibration lines obtained from this analysis (tp=8 min) is shown inFIG. 15B.

A “best” measurement time-point (tp_(best)), corresponding to “best”pair of slope and intercept values, is then selected based on agoodness-of-fit criterion, and the signal ratio for the test sample iscomputed according to Equation 1 from fluorescence measurements obtainedat the time-point coincident with the selected “best” time point. Thequantity of analyte IL-8 in a test sample j can then be calculated fromthe signal ratio of the test sample at best measurement time-point,SR(tp_(best))_(j), and “best” pair of slope, m (tp_(best)), andintercept, b(tp_(best)), values by means of Equation 3:

log([IL-8]_(j))={log(SR(tp _(best)))−b((tp _(best))}/m((tp_(best))  Equation 3.

Various statistical criteria may be employed to determine a “best”calibration line, or a corresponding “best” measurement time, tp_(best).A number of these statistical criteria have been described in U.S. Pat.No. 5,863,736 and No. 6,066,458. Other statistical methods for selectinga best time also may be employed.

Experimental procedures were performed as follows. Antibody-probeconjugates Ab1-SA-P1 and Ab2-P2 were as described in EXAMPLE 7. Standardsamples containing 10 mM Tris-EDTA buffer, 20 pM Ab1-SA-P1, 100 pMAb2-P2, 1 mg/mL BSA, 25 nM hybridization blocker oligonucleotideRDB-3p8, and IL-8 at 0.01, 0.1, 1.0, 10.0 and 100 pM were prepared.After incubating for 3 hours at room temperature, an aliquot of eachstandard sample was diluted 1:10 (v/v) into Tris-EDTA buffer containing0.1 mg/mL BSA and then further diluted 1:100 (v/v) into a solutioncontaining SDA primers (SRH-1 and SLH-2), adapter primers (adr-8 andadqs-2), reporter probes (TBD10.2(D/R) and ALTD6.9(F/D)), 50 nMhybridization blocker (RDB-3p8), and 100,000 copies of control nucleicacid (IQS-2). Two such diluted mixtures were prepared from each originalstandard sample. The diluted standard mixtures were then incubated at37° C. for approximately 10 minutes before an 80 μL aliquot of eachmixture was transferred into a separate microwell containing 20 μL ofSDA enzyme solution that had been pre-warmed to 52° C. The microwellswere then sealed, placed into a ProbeTec™ ET instrument and incubated at52° C. for 1 hour. During this 1-hour incubation, the fluorescence ofeach microwell was recorded through two optical channels, one specificfor rhodamine fluorescence and the other specific for fluoresceinfluorescence. A pair of fluorescence readings (one fluorescein and onerhodamine) was recorded at each 1-minute interval during the 1-hourcourse of the reaction, resulting in 60 pairs of fluorescence readingsfor each SDA reaction.

A set of test samples containing IL-8 concentrations of 0.01, 0.1, 1.0,10.0, and 100.0 pM were prepared and subjected to competitive two-colorSDA, as described above for the standard samples. The quantity ofcontrol oligonucleotide (IQS-2) was equivalent to those in the standardsamples.

In the present example, two-color fluorescence data from a total of 10duplicate SDA reactions for each of the five IL-8 standard samples wereused to construct a calibration equation as follows. For each of the 10amplified standard samples (i), signal ratios, SR(tp)_(i), werecalculated according to Equation 1 for each of the 60 time points (tp).Each set of coincident signal ratios from the standard samples wassubjected to linear regression against the known IL-8 concentration asdescribed in Equation 2 above, yielding slope (m(tp)) and intercept(b(tp)) values corresponding to a different “calibration” line for eachof the 60 time-points. A goodness-of-fit criterion was applied to thecalibration lines to determine that the best measurement time for thisplurality of standard samples was tp=8 minutes. A plot of log (SR(tp=8min)) versus log([IL-8]) and the corresponding calibration line areshown in FIG. 15B, which reveals a linear relationship between signalratio and IL-8 concentration over a 10,000-fold range of analyteconcentration.

Signal ratios were computed from fluorescence data (tp=8 minutes) forthe various test samples noted above. Equation 3 was then used tocalculate IL-8 concentrations of the test samples, using the best slopeand intercept values, corresponding to the tp=8 minutes calibration linederived from the standard curves.

The results shown in TABLE 16 reveal close agreement between calculatedand actual IL-8 concentrations, confirming the accurate quantificationof target analyte by methods of the present invention.

TABLE 16 Quantification of IL-8 in Test samples by immuno-SDA ActualIL-8 Calculated IL-8 Test Sample Concentration Concentration 1 0.01 pM0.02 pM 2 0.1 pM 0.09 pM 3 1.0 pM 0.9 pM 4 10 pM 6.8 pM 5 100 pM 92.0 pM

Having now fully described the invention with reference to certainrepresentative embodiments and details, it will be apparent to one ofordinary skill in the art that changes and modifications can be madethereto without departing from the spirit or scope of the invention asset forth herein. All the methods and procedures set forth herein arereadily practicable by the artisan of ordinary skill in this field.

1. A method of detecting an analyte, comprising: (i) combining: (a) ananalyte; (b) a first proximity member, comprising a firstanalyte-specific binding entity that is capable of forming a complexwith the analyte and that is conjugated to a first oligonucleotidemoiety comprising a first portion and a second portion; (c) a secondproximity member, comprising a second analyte-specific binding entitythat is capable of forming a complex with the analyte and that isconjugated to a second oligonucleotide moiety comprising a portion thatis capable of hybridizing to the first portion of the firstoligonucleotide; (d) a support comprising a capture oligonucleotide thatis capable of hybridizing to the second portion of the firstoligonucleotide moiety; (ii) forming a hybrid comprising the firstportion of the first oligonucleotide moiety and the portion of thesecond oligonucleotide moiety; (iii) extending the 3′ terminus toproduce an amplicon; (iv) amplifying the amplicon to produce anamplification product; and (v) detecting the amplification product;wherein detection of the amplification product allows detection of theanalyte.
 2. The method of claim 1, wherein the first and second portionsof the first oligonucleotide comprise no overlapping bases.
 3. Themethod of claim 1, wherein the first and second portions of the firstoligonucleotide comprise contiguous bases in common.
 4. The method ofclaim 1, wherein the first and second portions of the firstoligonucleotide are the same base sequence.
 5. The method of claim 1,wherein the hybrid comprises a 3′ terminus of the first or secondoligonucleotide moieties and said producing the amplicon comprisesextending the 3′ terminus.
 6. The method of claim 1, wherein saidproducing the amplicon comprises a ligation step.
 7. The method of claim1, comprising forming a hybrid between the capture oligonucleotide andthe first oligonucleotide moiety after said combining.
 8. The method ofclaim 7, further comprising washing the support after said forming ahybrid between the capture oligonucleotide and the first oligonucleotidemoiety.
 9. The method of claim 8, further comprising releasing the firstproximity member from the support after said washing the support. 10.The method of claim 9, wherein the hybrid between the captureoligonucleotide and the first oligonucleotide moiety comprises arestriction endonuclease recognition site, and wherein said releasingcomprises cleaving the site by a cognate restriction endonuclease. 11.The method of claim 9, further comprising a polymerase-catalyzedextension of the hybrid between the capture oligonucleotide and thefirst oligonucleotide moiety to form a restriction endonucleaserecognition site, wherein said releasing comprises cleaving the site bya cognate restriction endonuclease.
 12. The method of claim 9, whereinthe releasing is by physical dissociation of the hybrid between thecapture oligonucleotide and the first oligonucleotide moiety.
 13. Themethod of claim 9, wherein the releasing is by physical, chemical orenzymatic cleavage.
 14. The method of claim 9, wherein the releasingcomprises extending a double-stranded portion of the captureoligonucleotide to displace the first oligonucleotide moiety from thehybrid between the capture oligonucleotide and the first oligonucleotidemoiety.
 15. The method of claim 14, wherein the double-stranded portionof the capture oligonucleotide comprises a hairpin loop.
 16. The methodof claim 9, wherein the releasing comprises extending a double-strandedportion of the first oligonucleotide moiety to displace the captureoligonucleotide from the hybrid between the capture oligonucleotide andthe first oligonucleotide moiety.
 17. The method of 16, wherein thedouble-stranded portion comprises a hairpin loop.
 18. The method ofclaim 9, wherein one or both strands of the hybrid between the captureoligonucleotide and the first oligonucleotide moiety comprises RNA, andwherein the releasing comprises degrading said one or both strands witha RNase.
 19. The method of claim 1, wherein said amplifying is by amethod selected from the group consisting of polymerase chain reaction,strand displacement amplification, thermophilic strand displacementamplification, self-sustained sequence replication, nucleic acidsequence-based amplification, a Qβ replicase system, ligase chainreaction, and transcription mediated amplification.
 20. The method ofclaim 1, wherein the detecting is quantitative.
 21. A method ofdetecting an analyte, comprising: (i) combining: (a) an analyte; (b) afirst proximity member, comprising a first analyte-specific bindingentity that is capable of forming a complex with the analyte and that isconjugated to a tether oligonucleotide moiety comprising a first portionand a second portion; (c) a second proximity member, comprising a secondanalyte-specific binding entity that is capable of forming a complexwith the analyte and that is conjugated to an oligonucleotide moietycomprising a first portion; (d) a splint oligonucleotide, comprising (i)a first portion that is capable of hybridizing to the first portion ofthe oligonucleotide moiety and (ii) a second portion that is capable ofhybridizing to the first portion of the tether oligonucleotide moiety;(ii) forming: (a) a first hybrid comprising the first portion of theoligonucleotide moiety, the first portion of the splint oligonucleotide,and an extendable terminus of either the oligonucleotide moiety or thesplint oligonucleotide; and (b) a second hybrid comprising the firstportion of the tether oligonucleotide and the second portion of thetether oligonucleotide; (iii) extending the extendable terminus, therebyproducing an amplicon; (iv) amplifying the amplicon to produce anamplification product; and (v) detecting the amplification product;wherein detection of the amplification product allows detection of theanalyte.
 22. The method of claim 21, wherein the oligonucleotide moietycomprises the extendable terminus.
 23. The method of claim 21, whereinthe splint oligonucleotide comprises the extendable terminus.
 24. Themethod of claim 21, wherein said extending the extendable terminusdisplaces the tether oligonucleotide from the second hybrid.
 25. Themethod of claim 24, wherein the tether oligonucleotide is displaced bystrand displacement.
 26. The method of claim 24, wherein the tetheroligonucleotide is displaced by hydrolysis catalyzed by a polymerasehaving a 3′-5′ exonuclease activity.
 27. The method of claim 21, whereinsaid amplifying is by a method selected from the group consisting ofpolymerase chain reaction, strand displacement amplification,thermophilic strand displacement amplification, self-sustained sequencereplication, nucleic acid sequence-based amplification, a Qβ replicasesystem, ligase chain reaction, and transcription mediated amplification.28. The method of claim 21, wherein the splint oligonucleotide furthercomprises a restriction endonuclease recognition site located 3′ of thesecond portion and a first primer binding site located 3′ of therestriction endonuclease recognition site and 5′ of the first portion,and where the oligonucleotide moiety comprises a, second primer bindingsite located 5′ of the first portion of the oligonucleotide moiety. 29.The method of claim 28, wherein said amplifying is by stranddisplacement amplification comprising using first and second primersthat hybridize to the first and second primer binding sites,respectively, and a restriction endonuclease that nicks its cognaterecognition site.
 30. The method of claim 21, wherein the detecting isquantitative.
 31. The method of claim 21, wherein said producing theamplicon comprises a ligation step.
 32. A method of detecting ananalyte, comprising: (i) combining: (a) an analyte; (b) a firstproximity member, comprising a first analyte-specific binding entitythat is capable of forming a complex with the analyte and that isconjugated to a first tether oligonucleotide moiety comprising a firstportion; (c) a second proximity member, comprising a secondanalyte-specific binding entity that is capable of forming a complexwith the analyte and that is conjugated to a second tetheroligonucleotide moiety comprising a first portion; (d) a first splintoligonucleotide, comprising (i) a first portion that is capable ofhybridizing to the first portion of the first tether oligonucleotidemoiety and (ii) a second portion that is capable of hybridizing to asecond portion of a second splint oligonucleotide; (e) a second splintoligonucleotide, comprising (i) a first portion that is capablehybridizing to the first portion of the second tether oligonucleotidemoiety and (ii) a second portion that is capable of hybridizing to thesecond portion of the first splint oligonucleotide; (ii) forming: (a) afirst hybrid comprising the first portion of the first tetheroligonucleotide moiety and the first portion of the first splintoligonucleotide; (b) a second hybrid comprising the first portion of thesecond tether oligonucleotide and the first portion of the second splintoligonucleotide; and (c) a third hybrid comprising the second portionsof the first and second splint oligonucleotides, a 3′ terminus of thefirst splint oligonucleotide, and a 3′ terminus of the second splintoligonucleotide; (iii) extending the 3′ termini of the third hybrid,thereby producing an amplicon; (iv) amplifying the amplicon to producean amplification product; and (v) detecting the amplification product;wherein detection of the amplification product allows detection of theanalyte.
 33. The method of claim 32, wherein a 3′ terminus or a 5′terminus of the first tether oligonucleotide is conjugated to the firstanalyte-specific binding entity, and a 3′ terminus of the second tetheroligonucleotide is conjugated to the second analyte-specific bindingentity.
 34. The method of claim 32, wherein said producing an amplicondisplaces the first and second tether oligonucleotides from the firstand second hybrids.
 35. The method of claim 32, wherein the first andsecond tether oligonucleotides are displaced by strand displacement. 36.The method of claim 32, wherein the first and second tetheroligonucleotides are displaced by hydrolysis catalyzed by a polymerasehaving a 3′-5′ exonuclease activity.
 37. The method of claim 32, furthercomprising a wash step after said extending and before said amplifyingthat substantially removes the amplicon from the first and secondproximity members.
 38. The method of claim 32, wherein the detecting isquantitative.
 39. The method of claim 32, wherein said producing theamplicon comprises a ligation step.
 40. A method of detecting ananalyte, comprising: (i) combining: (a) an analyte; (b) a firstproximity member, comprising a first analyte-specific binding entitythat is capable of forming a complex with the analyte and that isconjugated to a first oligonucleotide moiety comprising a restrictionendonuclease recognition site, a 3′ cap that prevents 3′ extension ofthe first oligonucleotide moiety by a DNA polymerase, and a firstportion that is 3′ of the restriction endonuclease recognition site; (c)a second proximity member, comprising a second analyte-specific bindingentity that is capable of forming a complex with the analyte and that isconjugated to a second oligonucleotide moiety comprising a first portionthat is capable of forming a hybrid with the first portion of the firstoligonucleotide moiety; (ii) forming a hybrid comprising the firstportions of the first and second oligonucleotide moieties and a 3′terminus of the second oligonucleotide; (iii) extending the 3′ terminusof the second oligonucleotide moiety, thereby making the restrictionendonuclease recognition site of the first oligonucleotide moietydouble-stranded; (iv) nicking the restriction endonuclease recognitionsite of the first oligonucleotide moiety; (v) extending the firstoligonucleotide moiety from the nick to displace the downstream portionof the first oligonucleotide moiety; (vi) performing strand displacementamplification from the restriction endonuclease recognition site toproduce an amplification product; and (vii) detecting the amplificationproduct; wherein detection of the amplification product allows detectionof the analyte.
 41. The method of claim 40, wherein the secondoligonucleotide moiety comprises a restriction endonuclease recognitionsite, and the strand displacement amplification is from the restrictionendonuclease recognition sites of the first and second oligonucleotidemoieties.
 42. The method of claim 40, wherein the detecting isquantitative.
 43. The method of claim 40, wherein a 5′ terminus of thefirst oligonucleotide moiety is conjugated to the first analyte-specificbinding entity, and a 5′ terminus of the second oligonucleotide moietyis conjugated to the second analyte-specific binding entity.
 44. Amethod of detecting an analyte, comprising: (i) combining: (a) ananalyte comprising at least two antigen-specific binding sites; (b) afirst proximity member, comprising a first antigen that is conjugated toa first oligonucleotide moiety comprising a first portion, wherein thefirst antigen is capable of forming a complex with one of theantigen-binding sites of the analyte; (c) a second proximity member,comprising a second antigen that is conjugated to a secondoligonucleotide moiety comprising a first portion, wherein the secondantigen is capable of forming a complex with another antigen-bindingsite of the analyte; (ii) forming a hybrid comprising the first portionsof the first and second oligonucleotide moieties to produce an amplicon;(iii) amplifying the amplicon to produce an amplification product; and(iv) detecting the amplification product; wherein detection of theamplification product allows detection of the analyte.
 45. The method ofclaim 44, wherein the detecting is quantitative.
 46. The method of claim44, wherein the analyte is an antigen-specific immunoglobulin.
 47. Themethod of claim 44, wherein the hybrid comprises a 3′ terminus of thefirst or second oligonucleotide moieties.
 48. A kit, comprising: (a) afirst proximity member, comprising a first analyte-specific bindingentity that is capable of forming a complex with an analyte and that isconjugated to a first oligonucleotide moiety comprising a first portion;(b) a second proximity member, comprising a second analyte-specificbinding entity that is capable of forming a complex with the analyte andthat is conjugated to a second oligonucleotide moiety comprising aportion that is capable of hybridizing to the first portion of the firstoligonucleotide; and (c) a hybridization blocker oligonucleotide,wherein the hybridization blocker oligonucleotide comprises a portionthat is capable of forming a hybrid with the first portion of the firstoligonucleotide moiety.
 49. The kit of claim 48, wherein thehybridization blocker oligonucleotide comprises a 3′ sequence that isnot complementary to the first oligonucleotide moiety.
 50. The kit ofclaim 48, wherein the hybridization blocker oligonucleotide comprises a5′ sequence that is not complementary to the first oligonucleotidemoiety.
 51. The kit of claim 48, wherein the hybridization blockeroligonucleotide comprises a 3′ sequence and a 5′ sequence that are notcomplementary to the first oligonucleotide moiety.
 52. The kit of claim48, wherein the hybridization blocker oligonucleotide comprises a 3′ capthat prevents 3′ extension of the first oligonucleotide moiety by a DNApolymerase.
 53. The kit of claim 48, wherein the hybridization blockeroligonucleotide is capable of forming a hybrid comprising all of thefirst portion of the first oligonucleotide moiety.
 54. The kit of claim48, wherein the hybridization blocker oligonucleotide is capable offorming a hybrid comprising less than all of the first portion of thefirst oligonucleotide moiety.
 55. The kit of claim 48, furthercomprising a deblocker oligonucleotide that is capable of reducing thepresence of a hybrid between the hybridization blocker oligonucleotideand the first oligonucleotide.
 56. The kit of claim 55, wherein thedeblocker oligonucleotide comprises a first portion that is capable offorming a hybrid with the portion of the hybridization blockeroligonucleotide that is capable of forming a hybrid with the firstportion of the first oligonucleotide moiety.
 57. The kit of claim 56,wherein the deblocker oligonucleotide comprises a second portion that iscapable of forming a hybrid with a portion of the hybridization blockeroligonucleotide that does not form a hybrid with the firstoligonucleotide moiety.
 58. The kit of claim 57, wherein thehybridization blocker oligonucleotide comprises a double-strandedportion that is 3′ of the portion of the hybridization blocker that iscapable of forming a hybrid with the first portion of the firstoligonucleotide moiety.
 59. The kit of claim 58, wherein thedouble-stranded portion comprises a hairpin loop.
 60. The kit of claim48, further comprising a second hybridization blocker oligonucleotidethat is capable of hybridizing to the portion of the secondoligonucleotide moiety that is capable of forming a hybrid with thefirst portion of the first oligonucleotide moiety.
 61. A kit,comprising: (a) a first proximity member, comprising a firstanalyte-specific binding entity that is capable of forming a complexwith an analyte and that is conjugated to a first oligonucleotide moietycomprising a first portion and a second portion; (b) a second proximitymember, comprising a second analyte-specific binding entity that iscapable of forming a complex with the analyte and that is conjugated toa second oligonucleotide moiety comprising a portion that is capable ofhybridizing to the first portion of the first oligonucleotide; and (c) asupport comprising a capture oligonucleotide that is capable ofhybridizing to the second portion of the first oligonucleotide moiety.62. The kit of claim 61, wherein the first and second portions of thefirst oligonucleotide comprise no overlapping bases.
 63. The kit ofclaim 61, wherein the first and second portions of the firstoligonucleotide comprise contiguous bases in common.
 64. The kit ofclaim 61, wherein the first and second portions of the firstoligonucleotide are the same base sequence.
 65. The kit of claim 61,wherein the capture oligonucleotide or the first oligonucleotide moietycomprises one strand of a restriction endonuclease recognition site. 66.The kit of claim 61, wherein the capture oligonucleotide comprises adouble-stranded portion.
 67. The kit of claim 101, wherein thedouble-stranded portion of the capture oligonucleotide comprises ahairpin loop.
 68. The kit of claim 61, wherein the captureoligonucleotide comprises an RNA portion that is capable of forming ahybrid with the first oligonucleotide moiety.
 69. The kit of claim 61,wherein the first oligonucleotide moiety comprises an RNA portion thatis capable of forming a hybrid with the capture oligonucleotide.
 70. Akit, comprising: (a) a first proximity member, comprising a firstanalyte-specific binding entity that is capable of forming a complexwith an analyte and that is conjugated to a tether oligonucleotidemoiety comprising a first portion; (b) a second proximity member,comprising a second analyte-specific binding entity that is capable offorming a complex with the analyte and that is conjugated to anoligonucleotide moiety comprising a first portion; and (c) a splintoligonucleotide, comprising (i) a first portion that is capable ofhybridizing to the first portion of the oligonucleotide moiety and (ii)a second portion that is capable of hybridizing to the first portion ofthe tether oligonucleotide moiety.
 71. The kit of claim 70, wherein a 3′terminus of the tether oligonucleotide is conjugated to the firstanalyte-specific binding entity, and a 5′ terminus of theoligonucleotide moiety is conjugated to the second analyte-specificbinding entity.
 72. The kit of claim 70, wherein the splintoligonucleotide further comprises a restriction endonuclease recognitionsite located 3′ of the second portion and a first primer binding sitelocated 3′ of the restriction endonuclease recognition site and 5′ ofthe first portion, and wherein the oligonucleotide moiety comprises asecond primer binding site located 5′ of the first portion of theoligonucleotide moiety.
 73. A kit, comprising: (a) a first proximitymember, comprising a first analyte-specific binding entity that iscapable of forming a complex with an analyte and that is conjugated to afirst tether oligonucleotide moiety comprising a first portion; (b) asecond proximity member, comprising a second analyte-specific bindingentity that is capable of forming a complex with the analyte and that isconjugated to a second tether oligonucleotide moiety comprising a firstportion; (c) a first splint oligonucleotide, comprising (i) a firstportion that is capable of hybridizing to the first portion of the firsttether oligonucleotide moiety and (ii) a second portion that is capableof hybridizing to a second portion of a second splint oligonucleotide;and (d) a second splint oligonucleotide, comprising (i) a first portionthat is capable hybridizing to the first portion of the second tetheroligonucleotide moiety and (ii) a second portion that is capable ofhybridizing to the second portion of the first splint oligonucleotide.74. The kit of claim 73, wherein a 3′ or 5′ terminus of the first tetheroligonucleotide is conjugated to the first analyte-specific bindingentity, and a 3′ terminus of the second tether oligonucleotide isconjugated to the second analyte-specific binding entity.
 75. A kit,comprising: (a) a first proximity member, comprising a firstanalyte-specific binding entity that is capable of forming a complexwith an analyte and that is conjugated to a first oligonucleotide moietycomprising a restriction endonuclease recognition site, a 3′ cap thatprevents 3′ extension of the first oligonucleotide moiety by a DNApolymerase, and a first portion that is 3′ of the restrictionendonuclease recognition site; and (b) a second proximity member,comprising a second analyte-specific binding entity that is capable offorming a complex with the analyte and that is conjugated to a secondoligonucleotide moiety comprising a first portion that is capable offorming a hybrid with the first portion of the first oligonucleotidemoiety.
 76. The kit of claim 75, wherein the second oligonucleotidemoiety comprises a restriction endonuclease recognition site that is 5′of the first portion.
 77. The kit of claim 75, wherein a 5′ terminus ofthe first oligonucleotide moiety is conjugated to the firstanalyte-specific binding entity, and a 5′ terminus of the secondoligonucleotide moiety is conjugated to the second analyte-specificbinding entity.
 78. A kit, comprising: (a) a first proximity member,comprising a first antigen that is conjugated to a first oligonucleotidemoiety comprising a first portion, wherein the first antigen is capableof forming a complex with an antigen-binding site of an analytecomprising at least two antigen-specific binding sites; and (b) a secondproximity member, comprising a second antigen that is conjugated to asecond oligonucleotide moiety comprising a first portion, where thesecond antigen is capable of forming a complex with anotherantigen-binding site of the analyte.
 79. A method of quantifying anon-nucleic acid analyte, comprising: (i) forming a plurality ofstandard samples comprising (a) a first and second proximity member,each comprising an analyte-specific binding entity conjugated to anoligonucleotide moiety, (b) a known starting quantity of a nucleic acidcontrol, and (c) a known quantity of a non-nucleic acid analyte, therebyforming amplicons comprising a portion of the first and secondoligonucleotide moieties; (ii) forming at least one test samplecomprising (a) a first and second proximity member, each comprising ananalyte-specific binding entity conjugated to an oligonucleotide moiety,(b) the same known starting quantity of a nucleic acid control, and (c)an unknown quantity of the non-nucleic acid analyte, thereby forming anamplicon comprising a portion of the first and second oligonucleotidemoieties; (iii) amplifying the amplicons and the nucleic acid controls;(iv) measuring the amplified amplicons and nucleic acid controls todetermine a measured indicia; (v) determining a calibration curve fromthe measured indicia of the plurality of standard samples; and (vi)comparing the measured indicia of the at least one test sample with thecalibration curve to determine the quantity of the non-nucleic acidanalyte in the test sample.